diff --git a/api/server/controllers/PluginController.js b/api/server/controllers/PluginController.js
index e97afeccd..c5e074b8f 100644
--- a/api/server/controllers/PluginController.js
+++ b/api/server/controllers/PluginController.js
@@ -1,16 +1,9 @@
 const { logger } = require('@librechat/data-schemas');
-const { CacheKeys, Constants } = require('librechat-data-provider');
-const {
-  getToolkitKey,
-  checkPluginAuth,
-  filterUniquePlugins,
-  convertMCPToolToPlugin,
-  convertMCPToolsToPlugins,
-} = require('@librechat/api');
-const { getCachedTools, setCachedTools, mergeUserTools } = require('~/server/services/Config');
+const { CacheKeys } = require('librechat-data-provider');
+const { getToolkitKey, checkPluginAuth, filterUniquePlugins } = require('@librechat/api');
+const { getCachedTools, setCachedTools } = require('~/server/services/Config');
 const { availableTools, toolkits } = require('~/app/clients/tools');
 const { getAppConfig } = require('~/server/services/Config');
-const { getMCPManager } = require('~/config');
 const { getLogStores } = require('~/cache');
 
 const getAvailablePluginsController = async (req, res) => {
@@ -72,69 +65,27 @@ const getAvailableTools = async (req, res) => {
     }
     const cache = getLogStores(CacheKeys.CONFIG_STORE);
     const cachedToolsArray = await cache.get(CacheKeys.TOOLS);
-    const cachedUserTools = await getCachedTools({ userId });
 
     const appConfig = req.config ?? (await getAppConfig({ role: req.user?.role }));
 
-    /** @type {TPlugin[]} */
-    let mcpPlugins;
-    if (appConfig?.mcpConfig) {
-      const mcpManager = getMCPManager();
-      mcpPlugins =
-        cachedUserTools != null
-          ? convertMCPToolsToPlugins({ functionTools: cachedUserTools, mcpManager })
-          : undefined;
-    }
-
-    if (
-      cachedToolsArray != null &&
-      (appConfig?.mcpConfig != null ? mcpPlugins != null && mcpPlugins.length > 0 : true)
-    ) {
-      const dedupedTools = filterUniquePlugins([...(mcpPlugins ?? []), ...cachedToolsArray]);
-      res.status(200).json(dedupedTools);
+    // Return early if we have cached tools
+    if (cachedToolsArray != null) {
+      res.status(200).json(cachedToolsArray);
       return;
     }
 
     /** @type {Record<string, FunctionTool> | null} Get tool definitions to filter which tools are actually available */
-    let toolDefinitions = await getCachedTools({ includeGlobal: true });
-    let prelimCachedTools;
+    let toolDefinitions = await getCachedTools();
 
     if (toolDefinitions == null && appConfig?.availableTools != null) {
       logger.warn('[getAvailableTools] Tool cache was empty, re-initializing from app config');
-      await setCachedTools(appConfig.availableTools, { isGlobal: true });
+      await setCachedTools(appConfig.availableTools);
       toolDefinitions = appConfig.availableTools;
     }
 
     /** @type {import('@librechat/api').LCManifestTool[]} */
     let pluginManifest = availableTools;
 
-    if (appConfig?.mcpConfig != null) {
-      try {
-        const mcpManager = getMCPManager();
-        const mcpTools = await mcpManager.getAllToolFunctions(userId);
-        prelimCachedTools = prelimCachedTools ?? {};
-        for (const [toolKey, toolData] of Object.entries(mcpTools)) {
-          const plugin = convertMCPToolToPlugin({
-            toolKey,
-            toolData,
-            mcpManager,
-          });
-          if (plugin) {
-            pluginManifest.push(plugin);
-          }
-          prelimCachedTools[toolKey] = toolData;
-        }
-        await mergeUserTools({ userId, cachedUserTools, userTools: prelimCachedTools });
-      } catch (error) {
-        logger.error(
-          '[getAvailableTools] Error loading MCP Tools, servers may still be initializing:',
-          error,
-        );
-      }
-    } else if (prelimCachedTools != null) {
-      await setCachedTools(prelimCachedTools, { isGlobal: true });
-    }
-
     /** @type {TPlugin[]} Deduplicate and authenticate plugins */
     const uniquePlugins = filterUniquePlugins(pluginManifest);
     const authenticatedPlugins = uniquePlugins.map((plugin) => {
@@ -145,7 +96,7 @@ const getAvailableTools = async (req, res) => {
       }
     });
 
-    /** Filter plugins based on availability and add MCP-specific auth config */
+    /** Filter plugins based on availability */
     const toolsOutput = [];
     for (const plugin of authenticatedPlugins) {
       const isToolDefined = toolDefinitions?.[plugin.pluginKey] !== undefined;
@@ -159,39 +110,13 @@ const getAvailableTools = async (req, res) => {
         continue;
       }
 
-      const toolToAdd = { ...plugin };
-
-      if (plugin.pluginKey.includes(Constants.mcp_delimiter)) {
-        const parts = plugin.pluginKey.split(Constants.mcp_delimiter);
-        const serverName = parts[parts.length - 1];
-        const serverConfig = appConfig?.mcpConfig?.[serverName];
-
-        if (serverConfig?.customUserVars) {
-          const customVarKeys = Object.keys(serverConfig.customUserVars);
-          if (customVarKeys.length === 0) {
-            toolToAdd.authConfig = [];
-            toolToAdd.authenticated = true;
-          } else {
-            toolToAdd.authConfig = Object.entries(serverConfig.customUserVars).map(
-              ([key, value]) => ({
-                authField: key,
-                label: value.title || key,
-                description: value.description || '',
-              }),
-            );
-            toolToAdd.authenticated = false;
-          }
-        }
-      }
-
-      toolsOutput.push(toolToAdd);
+      toolsOutput.push(plugin);
     }
 
     const finalTools = filterUniquePlugins(toolsOutput);
     await cache.set(CacheKeys.TOOLS, finalTools);
 
-    const dedupedTools = filterUniquePlugins([...(mcpPlugins ?? []), ...finalTools]);
-    res.status(200).json(dedupedTools);
+    res.status(200).json(finalTools);
   } catch (error) {
     logger.error('[getAvailableTools]', error);
     res.status(500).json({ message: error.message });
diff --git a/api/server/controllers/PluginController.spec.js b/api/server/controllers/PluginController.spec.js
index cdbcabd75..d7d3f83a8 100644
--- a/api/server/controllers/PluginController.spec.js
+++ b/api/server/controllers/PluginController.spec.js
@@ -1,4 +1,3 @@
-const { Constants } = require('librechat-data-provider');
 const { getCachedTools, getAppConfig } = require('~/server/services/Config');
 const { getLogStores } = require('~/cache');
 
@@ -17,18 +16,10 @@ jest.mock('~/server/services/Config', () => ({
     includedTools: [],
   }),
   setCachedTools: jest.fn(),
-  mergeUserTools: jest.fn(),
 }));
 
 // loadAndFormatTools mock removed - no longer used in PluginController
-
-jest.mock('~/config', () => ({
-  getMCPManager: jest.fn(() => ({
-    getAllToolFunctions: jest.fn().mockResolvedValue({}),
-    getRawConfig: jest.fn().mockReturnValue({}),
-  })),
-  getFlowStateManager: jest.fn(),
-}));
+// getMCPManager mock removed - no longer used in PluginController
 
 jest.mock('~/app/clients/tools', () => ({
   availableTools: [],
@@ -159,52 +150,6 @@ describe('PluginController', () => {
   });
 
   describe('getAvailableTools', () => {
-    it('should use convertMCPToolsToPlugins for user-specific MCP tools', async () => {
-      const mockUserTools = {
-        [`tool1${Constants.mcp_delimiter}server1`]: {
-          type: 'function',
-          function: {
-            name: `tool1${Constants.mcp_delimiter}server1`,
-            description: 'Tool 1',
-            parameters: { type: 'object', properties: {} },
-          },
-        },
-      };
-
-      mockCache.get.mockResolvedValue(null);
-      getCachedTools.mockResolvedValueOnce(mockUserTools);
-      mockReq.config = {
-        mcpConfig: {
-          server1: {},
-        },
-        paths: { structuredTools: '/mock/path' },
-      };
-
-      // Mock MCP manager to return empty tools initially (since getAllToolFunctions is called)
-      const mockMCPManager = {
-        getAllToolFunctions: jest.fn().mockResolvedValue({}),
-        getRawConfig: jest.fn().mockReturnValue({}),
-      };
-      require('~/config').getMCPManager.mockReturnValue(mockMCPManager);
-
-      // Mock second call to return tool definitions (includeGlobal: true)
-      getCachedTools.mockResolvedValueOnce(mockUserTools);
-
-      await getAvailableTools(mockReq, mockRes);
-
-      expect(mockRes.status).toHaveBeenCalledWith(200);
-      const responseData = mockRes.json.mock.calls[0][0];
-      expect(responseData).toBeDefined();
-      expect(Array.isArray(responseData)).toBe(true);
-      expect(responseData.length).toBeGreaterThan(0);
-      const convertedTool = responseData.find(
-        (tool) => tool.pluginKey === `tool1${Constants.mcp_delimiter}server1`,
-      );
-      expect(convertedTool).toBeDefined();
-      // The real convertMCPToolsToPlugins extracts the name from the delimiter
-      expect(convertedTool.name).toBe('tool1');
-    });
-
     it('should use filterUniquePlugins to deduplicate combined tools', async () => {
       const mockUserTools = {
         'user-tool': {
@@ -229,9 +174,6 @@ describe('PluginController', () => {
         paths: { structuredTools: '/mock/path' },
       };
 
-      // Mock second call to return tool definitions
-      getCachedTools.mockResolvedValueOnce(mockUserTools);
-
       await getAvailableTools(mockReq, mockRes);
 
       expect(mockRes.status).toHaveBeenCalledWith(200);
@@ -254,14 +196,7 @@ describe('PluginController', () => {
       require('~/app/clients/tools').availableTools.push(mockPlugin);
 
       mockCache.get.mockResolvedValue(null);
-      // First call returns null for user tools
-      getCachedTools.mockResolvedValueOnce(null);
-      mockReq.config = {
-        mcpConfig: null,
-        paths: { structuredTools: '/mock/path' },
-      };
-
-      // Second call (with includeGlobal: true) returns the tool definitions
+      // getCachedTools returns the tool definitions
       getCachedTools.mockResolvedValueOnce({
         tool1: {
           type: 'function',
@@ -272,6 +207,10 @@ describe('PluginController', () => {
           },
         },
       });
+      mockReq.config = {
+        mcpConfig: null,
+        paths: { structuredTools: '/mock/path' },
+      };
 
       await getAvailableTools(mockReq, mockRes);
 
@@ -302,14 +241,7 @@ describe('PluginController', () => {
       });
 
       mockCache.get.mockResolvedValue(null);
-      // First call returns null for user tools
-      getCachedTools.mockResolvedValueOnce(null);
-      mockReq.config = {
-        mcpConfig: null,
-        paths: { structuredTools: '/mock/path' },
-      };
-
-      // Second call (with includeGlobal: true) returns the tool definitions
+      // getCachedTools returns the tool definitions
       getCachedTools.mockResolvedValueOnce({
         toolkit1_function: {
           type: 'function',
@@ -320,6 +252,10 @@ describe('PluginController', () => {
           },
         },
       });
+      mockReq.config = {
+        mcpConfig: null,
+        paths: { structuredTools: '/mock/path' },
+      };
 
       await getAvailableTools(mockReq, mockRes);
 
@@ -331,126 +267,7 @@ describe('PluginController', () => {
     });
   });
 
-  describe('plugin.icon behavior', () => {
-    const callGetAvailableToolsWithMCPServer = async (serverConfig) => {
-      mockCache.get.mockResolvedValue(null);
-
-      const functionTools = {
-        [`test-tool${Constants.mcp_delimiter}test-server`]: {
-          type: 'function',
-          function: {
-            name: `test-tool${Constants.mcp_delimiter}test-server`,
-            description: 'A test tool',
-            parameters: { type: 'object', properties: {} },
-          },
-        },
-      };
-
-      // Mock the MCP manager to return tools and server config
-      const mockMCPManager = {
-        getAllToolFunctions: jest.fn().mockResolvedValue(functionTools),
-        getRawConfig: jest.fn().mockReturnValue(serverConfig),
-      };
-      require('~/config').getMCPManager.mockReturnValue(mockMCPManager);
-
-      // First call returns empty user tools
-      getCachedTools.mockResolvedValueOnce({});
-
-      // Mock getAppConfig to return the mcpConfig
-      mockReq.config = {
-        mcpConfig: {
-          'test-server': serverConfig,
-        },
-      };
-
-      // Second call (with includeGlobal: true) returns the tool definitions
-      getCachedTools.mockResolvedValueOnce(functionTools);
-
-      await getAvailableTools(mockReq, mockRes);
-      const responseData = mockRes.json.mock.calls[0][0];
-      return responseData.find(
-        (tool) => tool.pluginKey === `test-tool${Constants.mcp_delimiter}test-server`,
-      );
-    };
-
-    it('should set plugin.icon when iconPath is defined', async () => {
-      const serverConfig = {
-        iconPath: '/path/to/icon.png',
-      };
-      const testTool = await callGetAvailableToolsWithMCPServer(serverConfig);
-      expect(testTool.icon).toBe('/path/to/icon.png');
-    });
-
-    it('should set plugin.icon to undefined when iconPath is not defined', async () => {
-      const serverConfig = {};
-      const testTool = await callGetAvailableToolsWithMCPServer(serverConfig);
-      expect(testTool.icon).toBeUndefined();
-    });
-  });
-
   describe('helper function integration', () => {
-    it('should properly handle MCP tools with custom user variables', async () => {
-      const appConfig = {
-        mcpConfig: {
-          'test-server': {
-            customUserVars: {
-              API_KEY: { title: 'API Key', description: 'Your API key' },
-            },
-          },
-        },
-      };
-
-      // Mock MCP tools returned by getAllToolFunctions
-      const mcpToolFunctions = {
-        [`tool1${Constants.mcp_delimiter}test-server`]: {
-          type: 'function',
-          function: {
-            name: `tool1${Constants.mcp_delimiter}test-server`,
-            description: 'Tool 1',
-            parameters: {},
-          },
-        },
-      };
-
-      // Mock the MCP manager to return tools
-      const mockMCPManager = {
-        getAllToolFunctions: jest.fn().mockResolvedValue(mcpToolFunctions),
-        getRawConfig: jest.fn().mockReturnValue({
-          customUserVars: {
-            API_KEY: { title: 'API Key', description: 'Your API key' },
-          },
-        }),
-      };
-      require('~/config').getMCPManager.mockReturnValue(mockMCPManager);
-
-      mockCache.get.mockResolvedValue(null);
-      mockReq.config = appConfig;
-
-      // First call returns user tools (empty in this case)
-      getCachedTools.mockResolvedValueOnce({});
-
-      // Second call (with includeGlobal: true) returns tool definitions including our MCP tool
-      getCachedTools.mockResolvedValueOnce(mcpToolFunctions);
-
-      await getAvailableTools(mockReq, mockRes);
-
-      expect(mockRes.status).toHaveBeenCalledWith(200);
-      const responseData = mockRes.json.mock.calls[0][0];
-      expect(Array.isArray(responseData)).toBe(true);
-
-      // Find the MCP tool in the response
-      const mcpTool = responseData.find(
-        (tool) => tool.pluginKey === `tool1${Constants.mcp_delimiter}test-server`,
-      );
-
-      // The actual implementation adds authConfig and sets authenticated to false when customUserVars exist
-      expect(mcpTool).toBeDefined();
-      expect(mcpTool.authConfig).toEqual([
-        { authField: 'API_KEY', label: 'API Key', description: 'Your API key' },
-      ]);
-      expect(mcpTool.authenticated).toBe(false);
-    });
-
     it('should handle error cases gracefully', async () => {
       mockCache.get.mockRejectedValue(new Error('Cache error'));
 
@@ -472,23 +289,13 @@ describe('PluginController', () => {
 
     it('should handle null cachedTools and cachedUserTools', async () => {
       mockCache.get.mockResolvedValue(null);
-      // First call returns null for user tools
-      getCachedTools.mockResolvedValueOnce(null);
+      // getCachedTools returns empty object instead of null
+      getCachedTools.mockResolvedValueOnce({});
       mockReq.config = {
         mcpConfig: null,
         paths: { structuredTools: '/mock/path' },
       };
 
-      // Mock MCP manager to return no tools
-      const mockMCPManager = {
-        getAllToolFunctions: jest.fn().mockResolvedValue({}),
-        getRawConfig: jest.fn().mockReturnValue({}),
-      };
-      require('~/config').getMCPManager.mockReturnValue(mockMCPManager);
-
-      // Second call (with includeGlobal: true) returns empty object instead of null
-      getCachedTools.mockResolvedValueOnce({});
-
       await getAvailableTools(mockReq, mockRes);
 
       // Should handle null values gracefully
@@ -503,9 +310,9 @@ describe('PluginController', () => {
         paths: { structuredTools: '/mock/path' },
       };
 
-      // Mock getCachedTools to return undefined for both calls
+      // Mock getCachedTools to return undefined
       getCachedTools.mockReset();
-      getCachedTools.mockResolvedValueOnce(undefined).mockResolvedValueOnce(undefined);
+      getCachedTools.mockResolvedValueOnce(undefined);
 
       await getAvailableTools(mockReq, mockRes);
 
@@ -514,51 +321,6 @@ describe('PluginController', () => {
       expect(mockRes.json).toHaveBeenCalledWith([]);
     });
 
-    it('should handle `cachedToolsArray` and `mcpPlugins` both being defined', async () => {
-      const cachedTools = [{ name: 'CachedTool', pluginKey: 'cached-tool', description: 'Cached' }];
-      // Use MCP delimiter for the user tool so convertMCPToolsToPlugins works
-      const userTools = {
-        [`user-tool${Constants.mcp_delimiter}server1`]: {
-          type: 'function',
-          function: {
-            name: `user-tool${Constants.mcp_delimiter}server1`,
-            description: 'User tool',
-            parameters: {},
-          },
-        },
-      };
-
-      mockCache.get.mockResolvedValue(cachedTools);
-      getCachedTools.mockResolvedValueOnce(userTools);
-      mockReq.config = {
-        mcpConfig: {
-          server1: {},
-        },
-        paths: { structuredTools: '/mock/path' },
-      };
-
-      // Mock MCP manager to return empty tools initially
-      const mockMCPManager = {
-        getAllToolFunctions: jest.fn().mockResolvedValue({}),
-        getRawConfig: jest.fn().mockReturnValue({}),
-      };
-      require('~/config').getMCPManager.mockReturnValue(mockMCPManager);
-
-      // The controller expects a second call to getCachedTools
-      getCachedTools.mockResolvedValueOnce({
-        'cached-tool': { type: 'function', function: { name: 'cached-tool' } },
-        [`user-tool${Constants.mcp_delimiter}server1`]:
-          userTools[`user-tool${Constants.mcp_delimiter}server1`],
-      });
-
-      await getAvailableTools(mockReq, mockRes);
-
-      expect(mockRes.status).toHaveBeenCalledWith(200);
-      const responseData = mockRes.json.mock.calls[0][0];
-      // Should have both cached and user tools
-      expect(responseData.length).toBeGreaterThanOrEqual(2);
-    });
-
     it('should handle empty toolDefinitions object', async () => {
       mockCache.get.mockResolvedValue(null);
       // Reset getCachedTools to ensure clean state
@@ -569,76 +331,12 @@ describe('PluginController', () => {
       // Ensure no plugins are available
       require('~/app/clients/tools').availableTools.length = 0;
 
-      // Reset MCP manager to default state
-      const mockMCPManager = {
-        getAllToolFunctions: jest.fn().mockResolvedValue({}),
-        getRawConfig: jest.fn().mockReturnValue({}),
-      };
-      require('~/config').getMCPManager.mockReturnValue(mockMCPManager);
-
       await getAvailableTools(mockReq, mockRes);
 
       // With empty tool definitions, no tools should be in the final output
       expect(mockRes.json).toHaveBeenCalledWith([]);
     });
 
-    it('should handle MCP tools without customUserVars', async () => {
-      const appConfig = {
-        mcpConfig: {
-          'test-server': {
-            // No customUserVars defined
-          },
-        },
-      };
-
-      const mockUserTools = {
-        [`tool1${Constants.mcp_delimiter}test-server`]: {
-          type: 'function',
-          function: {
-            name: `tool1${Constants.mcp_delimiter}test-server`,
-            description: 'Tool 1',
-            parameters: { type: 'object', properties: {} },
-          },
-        },
-      };
-
-      // Mock the MCP manager to return the tools
-      const mockMCPManager = {
-        getAllToolFunctions: jest.fn().mockResolvedValue(mockUserTools),
-        getRawConfig: jest.fn().mockReturnValue({
-          // No customUserVars defined
-        }),
-      };
-      require('~/config').getMCPManager.mockReturnValue(mockMCPManager);
-
-      mockCache.get.mockResolvedValue(null);
-      mockReq.config = appConfig;
-      // First call returns empty user tools
-      getCachedTools.mockResolvedValueOnce({});
-
-      // Second call (with includeGlobal: true) returns the tool definitions
-      getCachedTools.mockResolvedValueOnce(mockUserTools);
-
-      // Ensure no plugins in availableTools for clean test
-      require('~/app/clients/tools').availableTools.length = 0;
-
-      await getAvailableTools(mockReq, mockRes);
-
-      expect(mockRes.status).toHaveBeenCalledWith(200);
-      const responseData = mockRes.json.mock.calls[0][0];
-      expect(Array.isArray(responseData)).toBe(true);
-      expect(responseData.length).toBeGreaterThan(0);
-
-      const mcpTool = responseData.find(
-        (tool) => tool.pluginKey === `tool1${Constants.mcp_delimiter}test-server`,
-      );
-
-      expect(mcpTool).toBeDefined();
-      expect(mcpTool.authenticated).toBe(true);
-      // The actual implementation sets authConfig to empty array when no customUserVars
-      expect(mcpTool.authConfig).toEqual([]);
-    });
-
     it('should handle undefined filteredTools and includedTools', async () => {
       mockReq.config = {};
       mockCache.get.mockResolvedValue(null);
@@ -667,16 +365,13 @@ describe('PluginController', () => {
       require('~/app/clients/tools').availableTools.push(mockToolkit);
 
       mockCache.get.mockResolvedValue(null);
-      // First call returns empty object
+      // getCachedTools returns empty object to avoid null reference error
       getCachedTools.mockResolvedValueOnce({});
       mockReq.config = {
         mcpConfig: null,
         paths: { structuredTools: '/mock/path' },
       };
 
-      // Second call (with includeGlobal: true) returns empty object to avoid null reference error
-      getCachedTools.mockResolvedValueOnce({});
-
       await getAvailableTools(mockReq, mockRes);
 
       // Should handle null toolDefinitions gracefully
@@ -697,15 +392,12 @@ describe('PluginController', () => {
 
       mockCache.get.mockResolvedValue(null);
 
-      // First call returns null for user tools
-      getCachedTools.mockResolvedValueOnce(null);
-
       mockReq.config = {
         mcpConfig: null,
         paths: { structuredTools: '/mock/path' },
       };
 
-      // CRITICAL: Second call (with includeGlobal: true) returns undefined
+      // CRITICAL: getCachedTools returns undefined
       // This is what causes the bug when trying to access toolDefinitions[plugin.pluginKey]
       getCachedTools.mockResolvedValueOnce(undefined);
 
@@ -744,9 +436,8 @@ describe('PluginController', () => {
         { name: 'Tool 2', pluginKey: 'tool2', description: 'Tool 2' },
       );
 
-      // First call: Simulate cache cleared state (returns null for both global and user tools)
+      // Simulate cache cleared state (returns null)
       mockCache.get.mockResolvedValue(null);
-      getCachedTools.mockResolvedValueOnce(null); // User tools
       getCachedTools.mockResolvedValueOnce(null); // Global tools (cache cleared)
 
       mockReq.config = {
@@ -761,7 +452,7 @@ describe('PluginController', () => {
       await getAvailableTools(mockReq, mockRes);
 
       // Should have re-initialized the cache with tools from appConfig
-      expect(setCachedTools).toHaveBeenCalledWith(mockAppTools, { isGlobal: true });
+      expect(setCachedTools).toHaveBeenCalledWith(mockAppTools);
 
       // Should still return tools successfully
       expect(mockRes.status).toHaveBeenCalledWith(200);
@@ -784,7 +475,6 @@ describe('PluginController', () => {
 
       // Cache returns null (cleared state)
       mockCache.get.mockResolvedValue(null);
-      getCachedTools.mockResolvedValueOnce(null); // User tools
       getCachedTools.mockResolvedValueOnce(null); // Global tools (cache cleared)
 
       mockReq.config = {
diff --git a/api/server/controllers/UserController.js b/api/server/controllers/UserController.js
index e5c480c63..5d8dd9a5d 100644
--- a/api/server/controllers/UserController.js
+++ b/api/server/controllers/UserController.js
@@ -1,37 +1,34 @@
 const { logger } = require('@librechat/data-schemas');
+const { Tools, CacheKeys, Constants, FileSources } = require('librechat-data-provider');
 const {
   webSearchKeys,
-  extractWebSearchEnvVars,
-  normalizeHttpError,
+  MCPOAuthHandler,
   MCPTokenStorage,
+  normalizeHttpError,
+  extractWebSearchEnvVars,
 } = require('@librechat/api');
 const {
   getFiles,
+  findToken,
   updateUser,
   deleteFiles,
   deleteConvos,
   deletePresets,
   deleteMessages,
   deleteUserById,
+  deleteAllSharedLinks,
   deleteAllUserSessions,
 } = require('~/models');
 const { updateUserPluginAuth, deleteUserPluginAuth } = require('~/server/services/PluginService');
 const { updateUserPluginsService, deleteUserKey } = require('~/server/services/UserService');
 const { verifyEmail, resendVerificationEmail } = require('~/server/services/AuthService');
+const { getAppConfig, clearMCPServerTools } = require('~/server/services/Config');
 const { needsRefresh, getNewS3URL } = require('~/server/services/Files/S3/crud');
-const { Tools, Constants, FileSources } = require('librechat-data-provider');
 const { processDeleteRequest } = require('~/server/services/Files/process');
 const { Transaction, Balance, User, Token } = require('~/db/models');
-const { getAppConfig } = require('~/server/services/Config');
+const { getMCPManager, getFlowStateManager } = require('~/config');
 const { deleteToolCalls } = require('~/models/ToolCall');
-const { deleteAllSharedLinks } = require('~/models');
-const { getMCPManager } = require('~/config');
-const { MCPOAuthHandler } = require('@librechat/api');
-const { getFlowStateManager } = require('~/config');
-const { CacheKeys } = require('librechat-data-provider');
 const { getLogStores } = require('~/cache');
-const { clearMCPServerTools } = require('~/server/services/Config/mcpToolsCache');
-const { findToken } = require('~/models');
 
 const getUserController = async (req, res) => {
   const appConfig = await getAppConfig({ role: req.user?.role });
diff --git a/api/server/controllers/mcp.js b/api/server/controllers/mcp.js
new file mode 100644
index 000000000..40607a584
--- /dev/null
+++ b/api/server/controllers/mcp.js
@@ -0,0 +1,105 @@
+/**
+ * MCP Tools Controller
+ * Handles MCP-specific tool endpoints, decoupled from regular LibreChat tools
+ */
+const { logger } = require('@librechat/data-schemas');
+const { Constants } = require('librechat-data-provider');
+const { convertMCPToolToPlugin } = require('@librechat/api');
+const { getAppConfig, getMCPServerTools } = require('~/server/services/Config');
+const { getMCPManager } = require('~/config');
+
+/**
+ * Get all MCP tools available to the user
+ * Returns only MCP tools, not regular LibreChat tools
+ */
+const getMCPTools = async (req, res) => {
+  try {
+    const userId = req.user?.id;
+    if (!userId) {
+      logger.warn('[getMCPTools] User ID not found in request');
+      return res.status(401).json({ message: 'Unauthorized' });
+    }
+
+    const appConfig = req.config ?? (await getAppConfig({ role: req.user?.role }));
+    if (!appConfig?.mcpConfig) {
+      return res.status(200).json([]);
+    }
+
+    const mcpManager = getMCPManager();
+    const configuredServers = Object.keys(appConfig.mcpConfig);
+    const mcpTools = [];
+
+    // Fetch tools from each configured server
+    for (const serverName of configuredServers) {
+      try {
+        // First check server-specific cache
+        let serverTools = await getMCPServerTools(serverName);
+
+        if (!serverTools) {
+          // If not cached, fetch from MCP manager
+          const allTools = await mcpManager.getAllToolFunctions(userId);
+          serverTools = {};
+
+          // Filter tools for this specific server
+          for (const [toolKey, toolData] of Object.entries(allTools)) {
+            if (toolKey.endsWith(`${Constants.mcp_delimiter}${serverName}`)) {
+              serverTools[toolKey] = toolData;
+            }
+          }
+
+          // Cache server tools if found
+          if (Object.keys(serverTools).length > 0) {
+            const { cacheMCPServerTools } = require('~/server/services/Config');
+            await cacheMCPServerTools({ serverName, serverTools });
+          }
+        }
+
+        // Convert to plugin format
+        for (const [toolKey, toolData] of Object.entries(serverTools)) {
+          const plugin = convertMCPToolToPlugin({
+            toolKey,
+            toolData,
+            mcpManager,
+          });
+
+          if (plugin) {
+            // Add authentication config from server config
+            const serverConfig = appConfig.mcpConfig[serverName];
+            if (serverConfig?.customUserVars) {
+              const customVarKeys = Object.keys(serverConfig.customUserVars);
+              if (customVarKeys.length === 0) {
+                plugin.authConfig = [];
+                plugin.authenticated = true;
+              } else {
+                plugin.authConfig = Object.entries(serverConfig.customUserVars).map(
+                  ([key, value]) => ({
+                    authField: key,
+                    label: value.title || key,
+                    description: value.description || '',
+                  }),
+                );
+                plugin.authenticated = false;
+              }
+            } else {
+              plugin.authConfig = [];
+              plugin.authenticated = true;
+            }
+
+            mcpTools.push(plugin);
+          }
+        }
+      } catch (error) {
+        logger.error(`[getMCPTools] Error loading tools for server ${serverName}:`, error);
+      }
+    }
+
+    res.status(200).json(mcpTools);
+  } catch (error) {
+    logger.error('[getMCPTools]', error);
+    res.status(500).json({ message: error.message });
+  }
+};
+
+module.exports = {
+  getMCPTools,
+};
diff --git a/api/server/controllers/mcp.spec.js b/api/server/controllers/mcp.spec.js
new file mode 100644
index 000000000..6dea3ac34
--- /dev/null
+++ b/api/server/controllers/mcp.spec.js
@@ -0,0 +1,561 @@
+const { getMCPTools } = require('./mcp');
+const { getAppConfig, getMCPServerTools } = require('~/server/services/Config');
+const { getMCPManager } = require('~/config');
+const { convertMCPToolToPlugin } = require('@librechat/api');
+
+jest.mock('@librechat/data-schemas', () => ({
+  logger: {
+    debug: jest.fn(),
+    error: jest.fn(),
+    warn: jest.fn(),
+  },
+}));
+
+jest.mock('librechat-data-provider', () => ({
+  Constants: {
+    mcp_delimiter: '~~~',
+  },
+}));
+
+jest.mock('@librechat/api', () => ({
+  convertMCPToolToPlugin: jest.fn(),
+}));
+
+jest.mock('~/server/services/Config', () => ({
+  getAppConfig: jest.fn(),
+  getMCPServerTools: jest.fn(),
+  cacheMCPServerTools: jest.fn(),
+}));
+
+jest.mock('~/config', () => ({
+  getMCPManager: jest.fn(),
+}));
+
+describe('MCP Controller', () => {
+  let mockReq, mockRes, mockMCPManager;
+
+  beforeEach(() => {
+    jest.clearAllMocks();
+
+    mockReq = {
+      user: { id: 'test-user-id', role: 'user' },
+      config: null,
+    };
+
+    mockRes = {
+      status: jest.fn().mockReturnThis(),
+      json: jest.fn(),
+    };
+
+    mockMCPManager = {
+      getAllToolFunctions: jest.fn().mockResolvedValue({}),
+    };
+
+    getMCPManager.mockReturnValue(mockMCPManager);
+    getAppConfig.mockResolvedValue({
+      mcpConfig: {},
+    });
+    getMCPServerTools.mockResolvedValue(null);
+  });
+
+  describe('getMCPTools', () => {
+    it('should return 401 when user ID is not found', async () => {
+      mockReq.user = null;
+
+      await getMCPTools(mockReq, mockRes);
+
+      expect(mockRes.status).toHaveBeenCalledWith(401);
+      expect(mockRes.json).toHaveBeenCalledWith({ message: 'Unauthorized' });
+      const { logger } = require('@librechat/data-schemas');
+      expect(logger.warn).toHaveBeenCalledWith('[getMCPTools] User ID not found in request');
+    });
+
+    it('should return empty array when no mcpConfig exists', async () => {
+      getAppConfig.mockResolvedValue({
+        // No mcpConfig
+      });
+
+      await getMCPTools(mockReq, mockRes);
+
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([]);
+    });
+
+    it('should use cached server tools when available', async () => {
+      const cachedTools = {
+        'tool1~~~server1': {
+          type: 'function',
+          function: {
+            name: 'tool1',
+            description: 'Tool 1',
+            parameters: {},
+          },
+        },
+      };
+
+      getMCPServerTools.mockResolvedValue(cachedTools);
+      getAppConfig.mockResolvedValue({
+        mcpConfig: {
+          server1: {},
+        },
+      });
+
+      const mockPlugin = {
+        name: 'Tool 1',
+        pluginKey: 'tool1~~~server1',
+        description: 'Tool 1',
+      };
+      convertMCPToolToPlugin.mockReturnValue(mockPlugin);
+
+      await getMCPTools(mockReq, mockRes);
+
+      expect(getMCPServerTools).toHaveBeenCalledWith('server1');
+      expect(mockMCPManager.getAllToolFunctions).not.toHaveBeenCalled();
+      expect(convertMCPToolToPlugin).toHaveBeenCalledWith({
+        toolKey: 'tool1~~~server1',
+        toolData: cachedTools['tool1~~~server1'],
+        mcpManager: mockMCPManager,
+      });
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([
+        {
+          ...mockPlugin,
+          authConfig: [],
+          authenticated: true,
+        },
+      ]);
+    });
+
+    it('should fetch from MCP manager when cache is empty', async () => {
+      getMCPServerTools.mockResolvedValue(null);
+
+      const allTools = {
+        'tool1~~~server1': {
+          type: 'function',
+          function: {
+            name: 'tool1',
+            description: 'Tool 1',
+            parameters: {},
+          },
+        },
+        'tool2~~~server2': {
+          type: 'function',
+          function: {
+            name: 'tool2',
+            description: 'Tool 2',
+            parameters: {},
+          },
+        },
+      };
+
+      mockMCPManager.getAllToolFunctions.mockResolvedValue(allTools);
+
+      getAppConfig.mockResolvedValue({
+        mcpConfig: {
+          server1: {},
+        },
+      });
+
+      const mockPlugin = {
+        name: 'Tool 1',
+        pluginKey: 'tool1~~~server1',
+        description: 'Tool 1',
+      };
+      convertMCPToolToPlugin.mockReturnValue(mockPlugin);
+
+      await getMCPTools(mockReq, mockRes);
+
+      expect(getMCPServerTools).toHaveBeenCalledWith('server1');
+      expect(mockMCPManager.getAllToolFunctions).toHaveBeenCalledWith('test-user-id');
+
+      // Should cache the server tools
+      const { cacheMCPServerTools } = require('~/server/services/Config');
+      expect(cacheMCPServerTools).toHaveBeenCalledWith({
+        serverName: 'server1',
+        serverTools: {
+          'tool1~~~server1': allTools['tool1~~~server1'],
+        },
+      });
+
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([
+        {
+          ...mockPlugin,
+          authConfig: [],
+          authenticated: true,
+        },
+      ]);
+    });
+
+    it('should handle custom user variables in server config', async () => {
+      getMCPServerTools.mockResolvedValue({
+        'tool1~~~server1': {
+          type: 'function',
+          function: {
+            name: 'tool1',
+            description: 'Tool 1',
+            parameters: {},
+          },
+        },
+      });
+
+      getAppConfig.mockResolvedValue({
+        mcpConfig: {
+          server1: {
+            customUserVars: {
+              API_KEY: {
+                title: 'API Key',
+                description: 'Your API key',
+              },
+              SECRET: {
+                title: 'Secret Token',
+                description: 'Your secret token',
+              },
+            },
+          },
+        },
+      });
+
+      const mockPlugin = {
+        name: 'Tool 1',
+        pluginKey: 'tool1~~~server1',
+        description: 'Tool 1',
+      };
+      convertMCPToolToPlugin.mockReturnValue(mockPlugin);
+
+      await getMCPTools(mockReq, mockRes);
+
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([
+        {
+          ...mockPlugin,
+          authConfig: [
+            {
+              authField: 'API_KEY',
+              label: 'API Key',
+              description: 'Your API key',
+            },
+            {
+              authField: 'SECRET',
+              label: 'Secret Token',
+              description: 'Your secret token',
+            },
+          ],
+          authenticated: false,
+        },
+      ]);
+    });
+
+    it('should handle empty custom user variables', async () => {
+      getMCPServerTools.mockResolvedValue({
+        'tool1~~~server1': {
+          type: 'function',
+          function: {
+            name: 'tool1',
+            description: 'Tool 1',
+            parameters: {},
+          },
+        },
+      });
+
+      getAppConfig.mockResolvedValue({
+        mcpConfig: {
+          server1: {
+            customUserVars: {},
+          },
+        },
+      });
+
+      const mockPlugin = {
+        name: 'Tool 1',
+        pluginKey: 'tool1~~~server1',
+        description: 'Tool 1',
+      };
+      convertMCPToolToPlugin.mockReturnValue(mockPlugin);
+
+      await getMCPTools(mockReq, mockRes);
+
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([
+        {
+          ...mockPlugin,
+          authConfig: [],
+          authenticated: true,
+        },
+      ]);
+    });
+
+    it('should handle multiple servers', async () => {
+      getMCPServerTools.mockResolvedValue(null);
+
+      const allTools = {
+        'tool1~~~server1': {
+          type: 'function',
+          function: {
+            name: 'tool1',
+            description: 'Tool 1',
+            parameters: {},
+          },
+        },
+        'tool2~~~server2': {
+          type: 'function',
+          function: {
+            name: 'tool2',
+            description: 'Tool 2',
+            parameters: {},
+          },
+        },
+      };
+
+      mockMCPManager.getAllToolFunctions.mockResolvedValue(allTools);
+
+      getAppConfig.mockResolvedValue({
+        mcpConfig: {
+          server1: {},
+          server2: {},
+        },
+      });
+
+      const mockPlugin1 = {
+        name: 'Tool 1',
+        pluginKey: 'tool1~~~server1',
+        description: 'Tool 1',
+      };
+      const mockPlugin2 = {
+        name: 'Tool 2',
+        pluginKey: 'tool2~~~server2',
+        description: 'Tool 2',
+      };
+
+      convertMCPToolToPlugin.mockReturnValueOnce(mockPlugin1).mockReturnValueOnce(mockPlugin2);
+
+      await getMCPTools(mockReq, mockRes);
+
+      expect(getMCPServerTools).toHaveBeenCalledWith('server1');
+      expect(getMCPServerTools).toHaveBeenCalledWith('server2');
+      expect(mockMCPManager.getAllToolFunctions).toHaveBeenCalledTimes(2);
+
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([
+        {
+          ...mockPlugin1,
+          authConfig: [],
+          authenticated: true,
+        },
+        {
+          ...mockPlugin2,
+          authConfig: [],
+          authenticated: true,
+        },
+      ]);
+    });
+
+    it('should handle server-specific errors gracefully', async () => {
+      getMCPServerTools.mockResolvedValue(null);
+      mockMCPManager.getAllToolFunctions.mockRejectedValue(new Error('Server connection failed'));
+
+      getAppConfig.mockResolvedValue({
+        mcpConfig: {
+          server1: {},
+          server2: {},
+        },
+      });
+
+      await getMCPTools(mockReq, mockRes);
+
+      const { logger } = require('@librechat/data-schemas');
+      expect(logger.error).toHaveBeenCalledWith(
+        '[getMCPTools] Error loading tools for server server1:',
+        expect.any(Error),
+      );
+      expect(logger.error).toHaveBeenCalledWith(
+        '[getMCPTools] Error loading tools for server server2:',
+        expect.any(Error),
+      );
+
+      // Should still return 200 with empty array
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([]);
+    });
+
+    it('should skip tools when convertMCPToolToPlugin returns null', async () => {
+      getMCPServerTools.mockResolvedValue({
+        'tool1~~~server1': {
+          type: 'function',
+          function: {
+            name: 'tool1',
+            description: 'Tool 1',
+            parameters: {},
+          },
+        },
+        'tool2~~~server1': {
+          type: 'function',
+          function: {
+            name: 'tool2',
+            description: 'Tool 2',
+            parameters: {},
+          },
+        },
+      });
+
+      getAppConfig.mockResolvedValue({
+        mcpConfig: {
+          server1: {},
+        },
+      });
+
+      const mockPlugin = {
+        name: 'Tool 1',
+        pluginKey: 'tool1~~~server1',
+        description: 'Tool 1',
+      };
+
+      // First tool returns plugin, second returns null
+      convertMCPToolToPlugin.mockReturnValueOnce(mockPlugin).mockReturnValueOnce(null);
+
+      await getMCPTools(mockReq, mockRes);
+
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([
+        {
+          ...mockPlugin,
+          authConfig: [],
+          authenticated: true,
+        },
+      ]);
+    });
+
+    it('should use req.config when available', async () => {
+      const reqConfig = {
+        mcpConfig: {
+          server1: {},
+        },
+      };
+      mockReq.config = reqConfig;
+
+      getMCPServerTools.mockResolvedValue({
+        'tool1~~~server1': {
+          type: 'function',
+          function: {
+            name: 'tool1',
+            description: 'Tool 1',
+            parameters: {},
+          },
+        },
+      });
+
+      const mockPlugin = {
+        name: 'Tool 1',
+        pluginKey: 'tool1~~~server1',
+        description: 'Tool 1',
+      };
+      convertMCPToolToPlugin.mockReturnValue(mockPlugin);
+
+      await getMCPTools(mockReq, mockRes);
+
+      // Should not call getAppConfig when req.config is available
+      expect(getAppConfig).not.toHaveBeenCalled();
+
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([
+        {
+          ...mockPlugin,
+          authConfig: [],
+          authenticated: true,
+        },
+      ]);
+    });
+
+    it('should handle general error in getMCPTools', async () => {
+      const error = new Error('Unexpected error');
+      getAppConfig.mockRejectedValue(error);
+
+      await getMCPTools(mockReq, mockRes);
+
+      const { logger } = require('@librechat/data-schemas');
+      expect(logger.error).toHaveBeenCalledWith('[getMCPTools]', error);
+      expect(mockRes.status).toHaveBeenCalledWith(500);
+      expect(mockRes.json).toHaveBeenCalledWith({ message: 'Unexpected error' });
+    });
+
+    it('should handle custom user variables without title or description', async () => {
+      getMCPServerTools.mockResolvedValue({
+        'tool1~~~server1': {
+          type: 'function',
+          function: {
+            name: 'tool1',
+            description: 'Tool 1',
+            parameters: {},
+          },
+        },
+      });
+
+      getAppConfig.mockResolvedValue({
+        mcpConfig: {
+          server1: {
+            customUserVars: {
+              MY_VAR: {
+                // No title or description
+              },
+            },
+          },
+        },
+      });
+
+      const mockPlugin = {
+        name: 'Tool 1',
+        pluginKey: 'tool1~~~server1',
+        description: 'Tool 1',
+      };
+      convertMCPToolToPlugin.mockReturnValue(mockPlugin);
+
+      await getMCPTools(mockReq, mockRes);
+
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([
+        {
+          ...mockPlugin,
+          authConfig: [
+            {
+              authField: 'MY_VAR',
+              label: 'MY_VAR', // Falls back to key
+              description: '', // Empty string
+            },
+          ],
+          authenticated: false,
+        },
+      ]);
+    });
+
+    it('should not cache when no tools are found for a server', async () => {
+      getMCPServerTools.mockResolvedValue(null);
+
+      const allTools = {
+        'tool1~~~otherserver': {
+          type: 'function',
+          function: {
+            name: 'tool1',
+            description: 'Tool 1',
+            parameters: {},
+          },
+        },
+      };
+
+      mockMCPManager.getAllToolFunctions.mockResolvedValue(allTools);
+
+      getAppConfig.mockResolvedValue({
+        mcpConfig: {
+          server1: {},
+        },
+      });
+
+      await getMCPTools(mockReq, mockRes);
+
+      const { cacheMCPServerTools } = require('~/server/services/Config');
+      expect(cacheMCPServerTools).not.toHaveBeenCalled();
+
+      expect(mockRes.status).toHaveBeenCalledWith(200);
+      expect(mockRes.json).toHaveBeenCalledWith([]);
+    });
+  });
+});
diff --git a/api/server/routes/__tests__/mcp.spec.js b/api/server/routes/__tests__/mcp.spec.js
index b572340c5..1eb55224f 100644
--- a/api/server/routes/__tests__/mcp.spec.js
+++ b/api/server/routes/__tests__/mcp.spec.js
@@ -47,8 +47,8 @@ jest.mock('~/server/services/Config', () => ({
   loadCustomConfig: jest.fn(),
 }));
 
-jest.mock('~/server/services/Config/mcpToolsCache', () => ({
-  updateMCPUserTools: jest.fn(),
+jest.mock('~/server/services/Config/mcp', () => ({
+  updateMCPServerTools: jest.fn(),
 }));
 
 jest.mock('~/server/services/MCP', () => ({
@@ -778,10 +778,10 @@ describe('MCP Routes', () => {
       require('~/cache').getLogStores.mockReturnValue({});
 
       const { getCachedTools, setCachedTools } = require('~/server/services/Config');
-      const { updateMCPUserTools } = require('~/server/services/Config/mcpToolsCache');
+      const { updateMCPServerTools } = require('~/server/services/Config/mcp');
       getCachedTools.mockResolvedValue({});
       setCachedTools.mockResolvedValue();
-      updateMCPUserTools.mockResolvedValue();
+      updateMCPServerTools.mockResolvedValue();
 
       require('~/server/services/Tools/mcp').reinitMCPServer.mockResolvedValue({
         success: true,
@@ -836,10 +836,10 @@ describe('MCP Routes', () => {
       ]);
 
       const { getCachedTools, setCachedTools } = require('~/server/services/Config');
-      const { updateMCPUserTools } = require('~/server/services/Config/mcpToolsCache');
+      const { updateMCPServerTools } = require('~/server/services/Config/mcp');
       getCachedTools.mockResolvedValue({});
       setCachedTools.mockResolvedValue();
-      updateMCPUserTools.mockResolvedValue();
+      updateMCPServerTools.mockResolvedValue();
 
       require('~/server/services/Tools/mcp').reinitMCPServer.mockResolvedValue({
         success: true,
diff --git a/api/server/routes/mcp.js b/api/server/routes/mcp.js
index bff919158..fa0166830 100644
--- a/api/server/routes/mcp.js
+++ b/api/server/routes/mcp.js
@@ -5,15 +5,24 @@ const { MCPOAuthHandler, getUserMCPAuthMap } = require('@librechat/api');
 const { getMCPManager, getFlowStateManager, getOAuthReconnectionManager } = require('~/config');
 const { getMCPSetupData, getServerConnectionStatus } = require('~/server/services/MCP');
 const { findToken, updateToken, createToken, deleteTokens } = require('~/models');
-const { updateMCPUserTools } = require('~/server/services/Config/mcpToolsCache');
 const { getUserPluginAuthValue } = require('~/server/services/PluginService');
+const { updateMCPServerTools } = require('~/server/services/Config/mcp');
 const { reinitMCPServer } = require('~/server/services/Tools/mcp');
+const { getMCPTools } = require('~/server/controllers/mcp');
 const { requireJwtAuth } = require('~/server/middleware');
 const { findPluginAuthsByKeys } = require('~/models');
 const { getLogStores } = require('~/cache');
 
 const router = Router();
 
+/**
+ * Get all MCP tools available to the user
+ * Returns only MCP tools, completely decoupled from regular LibreChat tools
+ */
+router.get('/tools', requireJwtAuth, async (req, res) => {
+  return getMCPTools(req, res);
+});
+
 /**
  * Initiate OAuth flow
  * This endpoint is called when the user clicks the auth link in the UI
@@ -149,8 +158,7 @@ router.get('/:serverName/oauth/callback', async (req, res) => {
         oauthReconnectionManager.clearReconnection(flowState.userId, serverName);
 
         const tools = await userConnection.fetchTools();
-        await updateMCPUserTools({
-          userId: flowState.userId,
+        await updateMCPServerTools({
           serverName,
           tools,
         });
diff --git a/api/server/services/Config/app.js b/api/server/services/Config/app.js
index a5e771eff..ec6af7743 100644
--- a/api/server/services/Config/app.js
+++ b/api/server/services/Config/app.js
@@ -36,7 +36,7 @@ async function getAppConfig(options = {}) {
     }
 
     if (baseConfig.availableTools) {
-      await setCachedTools(baseConfig.availableTools, { isGlobal: true });
+      await setCachedTools(baseConfig.availableTools);
     }
 
     await cache.set(BASE_CONFIG_KEY, baseConfig);
diff --git a/api/server/services/Config/getCachedTools.js b/api/server/services/Config/getCachedTools.js
index 669c179a8..e33b2046a 100644
--- a/api/server/services/Config/getCachedTools.js
+++ b/api/server/services/Config/getCachedTools.js
@@ -3,89 +3,32 @@ const getLogStores = require('~/cache/getLogStores');
 
 /**
  * Cache key generators for different tool access patterns
- * These will support future permission-based caching
  */
 const ToolCacheKeys = {
   /** Global tools available to all users */
   GLOBAL: 'tools:global',
-  /** Tools available to a specific user */
-  USER: (userId) => `tools:user:${userId}`,
-  /** Tools available to a specific role */
-  ROLE: (roleId) => `tools:role:${roleId}`,
-  /** Tools available to a specific group */
-  GROUP: (groupId) => `tools:group:${groupId}`,
-  /** Combined effective tools for a user (computed from all sources) */
-  EFFECTIVE: (userId) => `tools:effective:${userId}`,
+  /** MCP tools cached by server name */
+  MCP_SERVER: (serverName) => `tools:mcp:${serverName}`,
 };
 
 /**
  * Retrieves available tools from cache
  * @function getCachedTools
  * @param {Object} options - Options for retrieving tools
- * @param {string} [options.userId] - User ID for user-specific tools
- * @param {string[]} [options.roleIds] - Role IDs for role-based tools
- * @param {string[]} [options.groupIds] - Group IDs for group-based tools
- * @param {boolean} [options.includeGlobal=true] - Whether to include global tools
+ * @param {string} [options.serverName] - MCP server name to get cached tools for
  * @returns {Promise<LCAvailableTools|null>} The available tools object or null if not cached
  */
 async function getCachedTools(options = {}) {
   const cache = getLogStores(CacheKeys.CONFIG_STORE);
-  const { userId, roleIds = [], groupIds = [], includeGlobal = true } = options;
+  const { serverName } = options;
 
-  // For now, return global tools (current behavior)
-  // This will be expanded to merge tools from different sources
-  if (!userId && includeGlobal) {
-    return await cache.get(ToolCacheKeys.GLOBAL);
+  // Return MCP server-specific tools if requested
+  if (serverName) {
+    return await cache.get(ToolCacheKeys.MCP_SERVER(serverName));
   }
 
-  // Future implementation will merge tools from multiple sources
-  // based on user permissions, roles, and groups
-  if (userId) {
-    /** @type {LCAvailableTools | null} Check if we have pre-computed effective tools for this user */
-    const effectiveTools = await cache.get(ToolCacheKeys.EFFECTIVE(userId));
-    if (effectiveTools) {
-      return effectiveTools;
-    }
-
-    /** @type {LCAvailableTools | null} Otherwise, compute from individual sources */
-    const toolSources = [];
-
-    if (includeGlobal) {
-      const globalTools = await cache.get(ToolCacheKeys.GLOBAL);
-      if (globalTools) {
-        toolSources.push(globalTools);
-      }
-    }
-
-    // User-specific tools
-    const userTools = await cache.get(ToolCacheKeys.USER(userId));
-    if (userTools) {
-      toolSources.push(userTools);
-    }
-
-    // Role-based tools
-    for (const roleId of roleIds) {
-      const roleTools = await cache.get(ToolCacheKeys.ROLE(roleId));
-      if (roleTools) {
-        toolSources.push(roleTools);
-      }
-    }
-
-    // Group-based tools
-    for (const groupId of groupIds) {
-      const groupTools = await cache.get(ToolCacheKeys.GROUP(groupId));
-      if (groupTools) {
-        toolSources.push(groupTools);
-      }
-    }
-
-    // Merge all tool sources (for now, simple merge - future will handle conflicts)
-    if (toolSources.length > 0) {
-      return mergeToolSources(toolSources);
-    }
-  }
-
-  return null;
+  // Default to global tools
+  return await cache.get(ToolCacheKeys.GLOBAL);
 }
 
 /**
@@ -93,49 +36,34 @@ async function getCachedTools(options = {}) {
  * @function setCachedTools
  * @param {Object} tools - The tools object to cache
  * @param {Object} options - Options for caching tools
- * @param {string} [options.userId] - User ID for user-specific tools
- * @param {string} [options.roleId] - Role ID for role-based tools
- * @param {string} [options.groupId] - Group ID for group-based tools
- * @param {boolean} [options.isGlobal=false] - Whether these are global tools
+ * @param {string} [options.serverName] - MCP server name for server-specific tools
  * @param {number} [options.ttl] - Time to live in milliseconds
  * @returns {Promise<boolean>} Whether the operation was successful
  */
 async function setCachedTools(tools, options = {}) {
   const cache = getLogStores(CacheKeys.CONFIG_STORE);
-  const { userId, roleId, groupId, isGlobal = false, ttl } = options;
+  const { serverName, ttl } = options;
 
-  let cacheKey;
-  if (isGlobal || (!userId && !roleId && !groupId)) {
-    cacheKey = ToolCacheKeys.GLOBAL;
-  } else if (userId) {
-    cacheKey = ToolCacheKeys.USER(userId);
-  } else if (roleId) {
-    cacheKey = ToolCacheKeys.ROLE(roleId);
-  } else if (groupId) {
-    cacheKey = ToolCacheKeys.GROUP(groupId);
+  // Cache by MCP server if specified
+  if (serverName) {
+    return await cache.set(ToolCacheKeys.MCP_SERVER(serverName), tools, ttl);
   }
 
-  if (!cacheKey) {
-    throw new Error('Invalid cache key options provided');
-  }
-
-  return await cache.set(cacheKey, tools, ttl);
+  // Default to global cache
+  return await cache.set(ToolCacheKeys.GLOBAL, tools, ttl);
 }
 
 /**
  * Invalidates cached tools
  * @function invalidateCachedTools
  * @param {Object} options - Options for invalidating tools
- * @param {string} [options.userId] - User ID to invalidate
- * @param {string} [options.roleId] - Role ID to invalidate
- * @param {string} [options.groupId] - Group ID to invalidate
+ * @param {string} [options.serverName] - MCP server name to invalidate
  * @param {boolean} [options.invalidateGlobal=false] - Whether to invalidate global tools
- * @param {boolean} [options.invalidateEffective=true] - Whether to invalidate effective tools
  * @returns {Promise<void>}
  */
 async function invalidateCachedTools(options = {}) {
   const cache = getLogStores(CacheKeys.CONFIG_STORE);
-  const { userId, roleId, groupId, invalidateGlobal = false, invalidateEffective = true } = options;
+  const { serverName, invalidateGlobal = false } = options;
 
   const keysToDelete = [];
 
@@ -143,116 +71,45 @@ async function invalidateCachedTools(options = {}) {
     keysToDelete.push(ToolCacheKeys.GLOBAL);
   }
 
-  if (userId) {
-    keysToDelete.push(ToolCacheKeys.USER(userId));
-    if (invalidateEffective) {
-      keysToDelete.push(ToolCacheKeys.EFFECTIVE(userId));
-    }
-  }
-
-  if (roleId) {
-    keysToDelete.push(ToolCacheKeys.ROLE(roleId));
-    // TODO: In future, invalidate all users with this role
-  }
-
-  if (groupId) {
-    keysToDelete.push(ToolCacheKeys.GROUP(groupId));
-    // TODO: In future, invalidate all users in this group
+  if (serverName) {
+    keysToDelete.push(ToolCacheKeys.MCP_SERVER(serverName));
   }
 
   await Promise.all(keysToDelete.map((key) => cache.delete(key)));
 }
 
 /**
- * Computes and caches effective tools for a user
- * @function computeEffectiveTools
- * @param {string} userId - The user ID
- * @param {Object} context - Context containing user's roles and groups
- * @param {string[]} [context.roleIds=[]] - User's role IDs
- * @param {string[]} [context.groupIds=[]] - User's group IDs
- * @param {number} [ttl] - Time to live for the computed result
- * @returns {Promise<Object>} The computed effective tools
+ * Gets MCP tools for a specific server from cache or merges with global tools
+ * @function getMCPServerTools
+ * @param {string} serverName - The MCP server name
+ * @returns {Promise<LCAvailableTools|null>} The available tools for the server
  */
-async function computeEffectiveTools(userId, context = {}, ttl) {
-  const { roleIds = [], groupIds = [] } = context;
+async function getMCPServerTools(serverName) {
+  const cache = getLogStores(CacheKeys.CONFIG_STORE);
+  const serverTools = await cache.get(ToolCacheKeys.MCP_SERVER(serverName));
 
-  // Get all tool sources
-  const tools = await getCachedTools({
-    userId,
-    roleIds,
-    groupIds,
-    includeGlobal: true,
-  });
-
-  if (tools) {
-    // Cache the computed result
-    const cache = getLogStores(CacheKeys.CONFIG_STORE);
-    await cache.set(ToolCacheKeys.EFFECTIVE(userId), tools, ttl);
+  if (serverTools) {
+    return serverTools;
   }
 
-  return tools;
-}
-
-/**
- * Merges multiple tool sources into a single tools object
- * @function mergeToolSources
- * @param {Object[]} sources - Array of tool objects to merge
- * @returns {Object} Merged tools object
- */
-function mergeToolSources(sources) {
-  // For now, simple merge that combines all tools
-  // Future implementation will handle:
-  // - Permission precedence (deny > allow)
-  // - Tool property conflicts
-  // - Metadata merging
-  const merged = {};
-
-  for (const source of sources) {
-    if (!source || typeof source !== 'object') {
-      continue;
-    }
-
-    for (const [toolId, toolConfig] of Object.entries(source)) {
-      // Simple last-write-wins for now
-      // Future: merge based on permission levels
-      merged[toolId] = toolConfig;
-    }
-  }
-
-  return merged;
+  return null;
 }
 
 /**
  * Middleware-friendly function to get tools for a request
  * @function getToolsForRequest
- * @param {Object} req - Express request object
+ * @param {Object} [req] - Express request object
  * @returns {Promise<Object|null>} Available tools for the request
  */
-async function getToolsForRequest(req) {
-  const userId = req.user?.id;
-
-  // For now, return global tools if no user
-  if (!userId) {
-    return getCachedTools({ includeGlobal: true });
-  }
-
-  // Future: Extract roles and groups from req.user
-  const roleIds = req.user?.roles || [];
-  const groupIds = req.user?.groups || [];
-
-  return getCachedTools({
-    userId,
-    roleIds,
-    groupIds,
-    includeGlobal: true,
-  });
+async function getToolsForRequest(_req) {
+  return getCachedTools();
 }
 
 module.exports = {
   ToolCacheKeys,
   getCachedTools,
   setCachedTools,
+  getMCPServerTools,
   getToolsForRequest,
   invalidateCachedTools,
-  computeEffectiveTools,
 };
diff --git a/api/server/services/Config/index.js b/api/server/services/Config/index.js
index f1767ddec..63c9108c9 100644
--- a/api/server/services/Config/index.js
+++ b/api/server/services/Config/index.js
@@ -1,7 +1,7 @@
 const appConfig = require('./app');
+const mcpToolsCache = require('./mcp');
 const { config } = require('./EndpointService');
 const getCachedTools = require('./getCachedTools');
-const mcpToolsCache = require('./mcpToolsCache');
 const loadCustomConfig = require('./loadCustomConfig');
 const loadConfigModels = require('./loadConfigModels');
 const loadDefaultModels = require('./loadDefaultModels');
diff --git a/api/server/services/Config/mcpToolsCache.js b/api/server/services/Config/mcp.js
similarity index 56%
rename from api/server/services/Config/mcpToolsCache.js
rename to api/server/services/Config/mcp.js
index d335868d8..aab2edf3c 100644
--- a/api/server/services/Config/mcpToolsCache.js
+++ b/api/server/services/Config/mcp.js
@@ -4,27 +4,20 @@ const { getCachedTools, setCachedTools } = require('./getCachedTools');
 const { getLogStores } = require('~/cache');
 
 /**
- * Updates MCP tools in the cache for a specific server and user
+ * Updates MCP tools in the cache for a specific server
  * @param {Object} params - Parameters for updating MCP tools
- * @param {string} params.userId - User ID
  * @param {string} params.serverName - MCP server name
  * @param {Array} params.tools - Array of tool objects from MCP server
  * @returns {Promise<LCAvailableTools>}
  */
-async function updateMCPUserTools({ userId, serverName, tools }) {
+async function updateMCPServerTools({ serverName, tools }) {
   try {
-    const userTools = await getCachedTools({ userId });
-
+    const serverTools = {};
     const mcpDelimiter = Constants.mcp_delimiter;
-    for (const key of Object.keys(userTools)) {
-      if (key.endsWith(`${mcpDelimiter}${serverName}`)) {
-        delete userTools[key];
-      }
-    }
 
     for (const tool of tools) {
-      const name = `${tool.name}${Constants.mcp_delimiter}${serverName}`;
-      userTools[name] = {
+      const name = `${tool.name}${mcpDelimiter}${serverName}`;
+      serverTools[name] = {
         type: 'function',
         ['function']: {
           name,
@@ -34,12 +27,12 @@ async function updateMCPUserTools({ userId, serverName, tools }) {
       };
     }
 
-    await setCachedTools(userTools, { userId });
+    await setCachedTools(serverTools, { serverName });
 
     const cache = getLogStores(CacheKeys.CONFIG_STORE);
     await cache.delete(CacheKeys.TOOLS);
-    logger.debug(`[MCP Cache] Updated ${tools.length} tools for ${serverName} user ${userId}`);
-    return userTools;
+    logger.debug(`[MCP Cache] Updated ${tools.length} tools for server ${serverName}`);
+    return serverTools;
   } catch (error) {
     logger.error(`[MCP Cache] Failed to update tools for ${serverName}:`, error);
     throw error;
@@ -57,9 +50,9 @@ async function mergeAppTools(appTools) {
     if (!count) {
       return;
     }
-    const cachedTools = await getCachedTools({ includeGlobal: true });
+    const cachedTools = await getCachedTools();
     const mergedTools = { ...cachedTools, ...appTools };
-    await setCachedTools(mergedTools, { isGlobal: true });
+    await setCachedTools(mergedTools);
     const cache = getLogStores(CacheKeys.CONFIG_STORE);
     await cache.delete(CacheKeys.TOOLS);
     logger.debug(`Merged ${count} app-level tools`);
@@ -70,30 +63,23 @@ async function mergeAppTools(appTools) {
 }
 
 /**
- * Merges user-level tools with global tools
+ * Caches MCP server tools (no longer merges with global)
  * @param {object} params
- * @param {string} params.userId
- * @param {Record<string, FunctionTool>} params.cachedUserTools
- * @param {import('@librechat/api').LCAvailableTools} params.userTools
+ * @param {string} params.serverName
+ * @param {import('@librechat/api').LCAvailableTools} params.serverTools
  * @returns {Promise<void>}
  */
-async function mergeUserTools({ userId, cachedUserTools, userTools }) {
+async function cacheMCPServerTools({ serverName, serverTools }) {
   try {
-    if (!userId) {
-      return;
-    }
-    const count = Object.keys(userTools).length;
+    const count = Object.keys(serverTools).length;
     if (!count) {
       return;
     }
-    const cachedTools = cachedUserTools ?? (await getCachedTools({ userId }));
-    const mergedTools = { ...cachedTools, ...userTools };
-    await setCachedTools(mergedTools, { userId });
-    const cache = getLogStores(CacheKeys.CONFIG_STORE);
-    await cache.delete(CacheKeys.TOOLS);
-    logger.debug(`Merged ${count} user-level tools`);
+    // Only cache server-specific tools, no merging with global
+    await setCachedTools(serverTools, { serverName });
+    logger.debug(`Cached ${count} MCP server tools for ${serverName}`);
   } catch (error) {
-    logger.error('Failed to merge user-level tools:', error);
+    logger.error(`Failed to cache MCP server tools for ${serverName}:`, error);
     throw error;
   }
 }
@@ -101,13 +87,12 @@ async function mergeUserTools({ userId, cachedUserTools, userTools }) {
 /**
  * Clears all MCP tools for a specific server
  * @param {Object} params - Parameters for clearing MCP tools
- * @param {string} [params.userId] - User ID (if clearing user-specific tools)
  * @param {string} params.serverName - MCP server name
  * @returns {Promise<void>}
  */
-async function clearMCPServerTools({ userId, serverName }) {
+async function clearMCPServerTools({ serverName }) {
   try {
-    const tools = await getCachedTools({ userId, includeGlobal: !userId });
+    const tools = await getCachedTools();
 
     // Remove all tools for this server
     const mcpDelimiter = Constants.mcp_delimiter;
@@ -120,14 +105,14 @@ async function clearMCPServerTools({ userId, serverName }) {
     }
 
     if (removedCount > 0) {
-      await setCachedTools(tools, userId ? { userId } : { isGlobal: true });
+      await setCachedTools(tools);
 
       const cache = getLogStores(CacheKeys.CONFIG_STORE);
       await cache.delete(CacheKeys.TOOLS);
+      // Also clear the server-specific cache
+      await cache.delete(`tools:mcp:${serverName}`);
 
-      logger.debug(
-        `[MCP Cache] Removed ${removedCount} tools for ${serverName}${userId ? ` user ${userId}` : ' (global)'}`,
-      );
+      logger.debug(`[MCP Cache] Removed ${removedCount} tools for ${serverName} (global)`);
     }
   } catch (error) {
     logger.error(`[MCP Cache] Failed to clear tools for ${serverName}:`, error);
@@ -137,7 +122,7 @@ async function clearMCPServerTools({ userId, serverName }) {
 
 module.exports = {
   mergeAppTools,
-  mergeUserTools,
-  updateMCPUserTools,
+  cacheMCPServerTools,
   clearMCPServerTools,
+  updateMCPServerTools,
 };
diff --git a/api/server/services/Tools/mcp.js b/api/server/services/Tools/mcp.js
index 069447e3b..c9c369868 100644
--- a/api/server/services/Tools/mcp.js
+++ b/api/server/services/Tools/mcp.js
@@ -2,7 +2,7 @@ const { logger } = require('@librechat/data-schemas');
 const { CacheKeys, Constants } = require('librechat-data-provider');
 const { findToken, createToken, updateToken, deleteTokens } = require('~/models');
 const { getMCPManager, getFlowStateManager } = require('~/config');
-const { updateMCPUserTools } = require('~/server/services/Config');
+const { updateMCPServerTools } = require('~/server/services/Config');
 const { getLogStores } = require('~/cache');
 
 /**
@@ -97,8 +97,7 @@ async function reinitMCPServer({
 
     if (userConnection && !oauthRequired) {
       tools = await userConnection.fetchTools();
-      availableTools = await updateMCPUserTools({
-        userId: req.user.id,
+      availableTools = await updateMCPServerTools({
         serverName,
         tools,
       });
diff --git a/client/src/Providers/AgentPanelContext.tsx b/client/src/Providers/AgentPanelContext.tsx
index 135066c78..e97e25403 100644
--- a/client/src/Providers/AgentPanelContext.tsx
+++ b/client/src/Providers/AgentPanelContext.tsx
@@ -1,14 +1,16 @@
 import React, { createContext, useContext, useState, useMemo } from 'react';
 import { Constants, EModelEndpoint } from 'librechat-data-provider';
-import type { MCP, Action, TPlugin, AgentToolType } from 'librechat-data-provider';
+import type { MCP, Action, TPlugin } from 'librechat-data-provider';
 import type { AgentPanelContextType, MCPServerInfo } from '~/common';
-import { useAvailableToolsQuery, useGetActionsQuery, useGetStartupConfig } from '~/data-provider';
+import {
+  useAvailableToolsQuery,
+  useGetActionsQuery,
+  useGetStartupConfig,
+  useMCPToolsQuery,
+} from '~/data-provider';
 import { useLocalize, useGetAgentsConfig, useMCPConnectionStatus } from '~/hooks';
 import { Panel } from '~/common';
 
-type GroupedToolType = AgentToolType & { tools?: AgentToolType[] };
-type GroupedToolsRecord = Record<string, GroupedToolType>;
-
 const AgentPanelContext = createContext<AgentPanelContextType | undefined>(undefined);
 
 export function useAgentPanelContext() {
@@ -32,11 +34,16 @@ export function AgentPanelProvider({ children }: { children: React.ReactNode })
     enabled: !!agent_id,
   });
 
-  const { data: pluginTools } = useAvailableToolsQuery(EModelEndpoint.agents, {
+  const { data: regularTools } = useAvailableToolsQuery(EModelEndpoint.agents, {
+    enabled: !!agent_id,
+  });
+
+  const { data: mcpTools } = useMCPToolsQuery({
     enabled: !!agent_id,
   });
 
   const { data: startupConfig } = useGetStartupConfig();
+  const { agentsConfig, endpointsConfig } = useGetAgentsConfig();
   const mcpServerNames = useMemo(
     () => Object.keys(startupConfig?.mcpServers ?? {}),
     [startupConfig],
@@ -46,61 +53,43 @@ export function AgentPanelProvider({ children }: { children: React.ReactNode })
     enabled: !!agent_id && mcpServerNames.length > 0,
   });
 
-  const processedData = useMemo(() => {
-    if (!pluginTools) {
-      return {
-        tools: [],
-        groupedTools: {},
-        mcpServersMap: new Map<string, MCPServerInfo>(),
-      };
-    }
-
-    const tools: AgentToolType[] = [];
-    const groupedTools: GroupedToolsRecord = {};
-
+  const mcpServersMap = useMemo(() => {
     const configuredServers = new Set(mcpServerNames);
-    const mcpServersMap = new Map<string, MCPServerInfo>();
+    const serversMap = new Map<string, MCPServerInfo>();
 
-    for (const pluginTool of pluginTools) {
-      const tool: AgentToolType = {
-        tool_id: pluginTool.pluginKey,
-        metadata: pluginTool as TPlugin,
-      };
+    if (mcpTools) {
+      for (const pluginTool of mcpTools) {
+        if (pluginTool.pluginKey.includes(Constants.mcp_delimiter)) {
+          const [_toolName, serverName] = pluginTool.pluginKey.split(Constants.mcp_delimiter);
 
-      tools.push(tool);
+          if (!serversMap.has(serverName)) {
+            const metadata = {
+              name: serverName,
+              pluginKey: serverName,
+              description: `${localize('com_ui_tool_collection_prefix')} ${serverName}`,
+              icon: pluginTool.icon || '',
+            } as TPlugin;
 
-      if (tool.tool_id.includes(Constants.mcp_delimiter)) {
-        const [_toolName, serverName] = tool.tool_id.split(Constants.mcp_delimiter);
+            serversMap.set(serverName, {
+              serverName,
+              tools: [],
+              isConfigured: configuredServers.has(serverName),
+              isConnected: connectionStatus?.[serverName]?.connectionState === 'connected',
+              metadata,
+            });
+          }
 
-        if (!mcpServersMap.has(serverName)) {
-          const metadata = {
-            name: serverName,
-            pluginKey: serverName,
-            description: `${localize('com_ui_tool_collection_prefix')} ${serverName}`,
-            icon: pluginTool.icon || '',
-          } as TPlugin;
-
-          mcpServersMap.set(serverName, {
-            serverName,
-            tools: [],
-            isConfigured: configuredServers.has(serverName),
-            isConnected: connectionStatus?.[serverName]?.connectionState === 'connected',
-            metadata,
+          serversMap.get(serverName)!.tools.push({
+            tool_id: pluginTool.pluginKey,
+            metadata: pluginTool as TPlugin,
           });
         }
-
-        mcpServersMap.get(serverName)!.tools.push(tool);
-      } else {
-        // Non-MCP tool
-        groupedTools[tool.tool_id] = {
-          tool_id: tool.tool_id,
-          metadata: tool.metadata,
-        };
       }
     }
 
+    // Add configured servers that don't have tools yet
     for (const mcpServerName of mcpServerNames) {
-      if (mcpServersMap.has(mcpServerName)) {
+      if (serversMap.has(mcpServerName)) {
         continue;
       }
       const metadata = {
@@ -110,7 +99,7 @@ export function AgentPanelProvider({ children }: { children: React.ReactNode })
         description: `${localize('com_ui_tool_collection_prefix')} ${mcpServerName}`,
       } as TPlugin;
 
-      mcpServersMap.set(mcpServerName, {
+      serversMap.set(mcpServerName, {
         tools: [],
         metadata,
         isConfigured: true,
@@ -119,14 +108,8 @@ export function AgentPanelProvider({ children }: { children: React.ReactNode })
       });
     }
 
-    return {
-      tools,
-      groupedTools,
-      mcpServersMap,
-    };
-  }, [pluginTools, localize, mcpServerNames, connectionStatus]);
-
-  const { agentsConfig, endpointsConfig } = useGetAgentsConfig();
+    return serversMap;
+  }, [mcpTools, localize, mcpServerNames, connectionStatus]);
 
   const value: AgentPanelContextType = {
     mcp,
@@ -137,16 +120,15 @@ export function AgentPanelProvider({ children }: { children: React.ReactNode })
     setMcps,
     agent_id,
     setAction,
-    pluginTools,
+    mcpTools,
     activePanel,
+    regularTools,
     agentsConfig,
     startupConfig,
+    mcpServersMap,
     setActivePanel,
     endpointsConfig,
     setCurrentAgentId,
-    tools: processedData.tools,
-    groupedTools: processedData.groupedTools,
-    mcpServersMap: processedData.mcpServersMap,
   };
 
   return <AgentPanelContext.Provider value={value}>{children}</AgentPanelContext.Provider>;
diff --git a/client/src/common/types.ts b/client/src/common/types.ts
index 5ea6ad6bb..211c7a7a7 100644
--- a/client/src/common/types.ts
+++ b/client/src/common/types.ts
@@ -232,10 +232,9 @@ export type AgentPanelContextType = {
   mcps?: t.MCP[];
   setMcp: React.Dispatch<React.SetStateAction<t.MCP | undefined>>;
   setMcps: React.Dispatch<React.SetStateAction<t.MCP[] | undefined>>;
-  groupedTools: Record<string, t.AgentToolType & { tools?: t.AgentToolType[] }>;
   activePanel?: string;
-  tools: t.AgentToolType[];
-  pluginTools?: t.TPlugin[];
+  regularTools?: t.TPlugin[];
+  mcpTools?: t.TPlugin[];
   setActivePanel: React.Dispatch<React.SetStateAction<Panel>>;
   setCurrentAgentId: React.Dispatch<React.SetStateAction<string | undefined>>;
   agent_id?: string;
diff --git a/client/src/components/SidePanel/Agents/AgentConfig.tsx b/client/src/components/SidePanel/Agents/AgentConfig.tsx
index 7f296fe8c..dcb047374 100644
--- a/client/src/components/SidePanel/Agents/AgentConfig.tsx
+++ b/client/src/components/SidePanel/Agents/AgentConfig.tsx
@@ -48,12 +48,12 @@ export default function AgentConfig({ createMutation }: Pick<AgentPanelProps, 'c
   const {
     actions,
     setAction,
+    regularTools,
     agentsConfig,
     startupConfig,
     mcpServersMap,
     setActivePanel,
     endpointsConfig,
-    groupedTools: allTools,
   } = useAgentPanelContext();
 
   const {
@@ -177,7 +177,7 @@ export default function AgentConfig({ createMutation }: Pick<AgentPanelProps, 'c
     Icon = icons[iconKey];
   }
 
-  const { toolIds, mcpServerNames } = useVisibleTools(tools, allTools, mcpServersMap);
+  const { toolIds, mcpServerNames } = useVisibleTools(tools, regularTools, mcpServersMap);
 
   return (
     <>
@@ -326,16 +326,15 @@ export default function AgentConfig({ createMutation }: Pick<AgentPanelProps, 'c
           </label>
           <div>
             <div className="mb-1">
-              {/* Render all visible IDs (including groups with subtools selected) */}
+              {/* Render all visible IDs */}
               {toolIds.map((toolId, i) => {
-                if (!allTools) return null;
-                const tool = allTools[toolId];
+                const tool = regularTools?.find((t) => t.pluginKey === toolId);
                 if (!tool) return null;
                 return (
                   <AgentTool
                     key={`${toolId}-${i}-${agent_id}`}
                     tool={toolId}
-                    allTools={allTools}
+                    regularTools={regularTools}
                     agent_id={agent_id}
                   />
                 );
diff --git a/client/src/components/SidePanel/Agents/AgentTool.tsx b/client/src/components/SidePanel/Agents/AgentTool.tsx
index 07857c7be..5685506fe 100644
--- a/client/src/components/SidePanel/Agents/AgentTool.tsx
+++ b/client/src/components/SidePanel/Agents/AgentTool.tsx
@@ -1,68 +1,47 @@
 import React, { useState } from 'react';
-import * as Ariakit from '@ariakit/react';
-import { ChevronDown } from 'lucide-react';
 import { useFormContext } from 'react-hook-form';
-import * as AccordionPrimitive from '@radix-ui/react-accordion';
 import { useUpdateUserPluginsMutation } from 'librechat-data-provider/react-query';
 import {
-  Accordion,
-  AccordionItem,
-  AccordionContent,
+  OGDialog,
   TrashIcon,
   CircleHelpIcon,
-  OGDialog,
-  OGDialogTrigger,
-  Label,
-  Checkbox,
-  OGDialogTemplate,
   useToastContext,
+  OGDialogTrigger,
+  OGDialogTemplate,
 } from '@librechat/client';
-import type { AgentToolType } from 'librechat-data-provider';
+import type { TPlugin } from 'librechat-data-provider';
 import type { AgentForm } from '~/common';
 import { useLocalize } from '~/hooks';
 import { cn } from '~/utils';
 
 export default function AgentTool({
   tool,
-  allTools,
+  regularTools,
 }: {
   tool: string;
-  allTools?: Record<string, AgentToolType & { tools?: AgentToolType[] }>;
+  regularTools?: TPlugin[];
   agent_id?: string;
 }) {
-  const [isHovering, setIsHovering] = useState(false);
-  const [isFocused, setIsFocused] = useState(false);
-  const [hoveredToolId, setHoveredToolId] = useState<string | null>(null);
-  const [accordionValue, setAccordionValue] = useState<string>('');
   const localize = useLocalize();
   const { showToast } = useToastContext();
   const updateUserPlugins = useUpdateUserPluginsMutation();
   const { getValues, setValue } = useFormContext<AgentForm>();
-  if (!allTools) {
+
+  const [isFocused, setIsFocused] = useState(false);
+  const [isHovering, setIsHovering] = useState(false);
+
+  if (!regularTools) {
     return null;
   }
-  const currentTool = allTools[tool];
-  const getSelectedTools = () => {
-    if (!currentTool?.tools) return [];
-    const formTools = getValues('tools') || [];
-    return currentTool.tools.filter((t) => formTools.includes(t.tool_id)).map((t) => t.tool_id);
-  };
 
-  const updateFormTools = (newSelectedTools: string[]) => {
-    const currentTools = getValues('tools') || [];
-    const otherTools = currentTools.filter(
-      (t: string) => !currentTool?.tools?.some((st) => st.tool_id === t),
-    );
-    setValue('tools', [...otherTools, ...newSelectedTools]);
-  };
+  const currentTool = regularTools.find((t) => t.pluginKey === tool);
+
+  if (!currentTool) {
+    return null;
+  }
 
   const removeTool = (toolId: string) => {
     if (toolId) {
-      const toolIdsToRemove =
-        isGroup && currentTool.tools
-          ? [toolId, ...currentTool.tools.map((t) => t.tool_id)]
-          : [toolId];
-
       updateUserPlugins.mutate(
         { pluginKey: toolId, action: 'uninstall', auth: {}, isEntityTool: true },
         {
@@ -70,9 +49,7 @@ export default function AgentTool({
             showToast({ message: `Error while deleting the tool: ${error}`, status: 'error' });
           },
           onSuccess: () => {
-            const remainingToolIds = getValues('tools')?.filter(
-              (toolId: string) => !toolIdsToRemove.includes(toolId),
-            );
+            const remainingToolIds = getValues('tools')?.filter((id: string) => id !== toolId);
             setValue('tools', remainingToolIds);
             showToast({ message: 'Tool deleted successfully', status: 'success' });
           },
@@ -81,327 +58,82 @@ export default function AgentTool({
     }
   };
 
-  if (!currentTool) {
-    return null;
-  }
-
-  const isGroup = currentTool.tools && currentTool.tools.length > 0;
-  const selectedTools = getSelectedTools();
-  const isExpanded = accordionValue === currentTool.tool_id;
-
-  if (!isGroup) {
-    return (
-      <OGDialog>
-        <div
-          className="group relative flex w-full items-center gap-1 rounded-lg p-1 text-sm hover:bg-gray-50 dark:hover:bg-gray-800/50"
-          onMouseEnter={() => setIsHovering(true)}
-          onMouseLeave={() => setIsHovering(false)}
-          onFocus={() => setIsFocused(true)}
-          onBlur={(e) => {
-            // Check if focus is moving to a child element
-            if (!e.currentTarget.contains(e.relatedTarget)) {
-              setIsFocused(false);
-            }
-          }}
-        >
-          <div className="flex grow items-center">
-            {currentTool.metadata.icon && (
-              <div className="flex h-8 w-8 items-center justify-center overflow-hidden rounded-full">
-                <div
-                  className="flex h-6 w-6 items-center justify-center overflow-hidden rounded-full bg-center bg-no-repeat dark:bg-white/20"
-                  style={{
-                    backgroundImage: `url(${currentTool.metadata.icon})`,
-                    backgroundSize: 'cover',
-                  }}
-                />
-              </div>
-            )}
-            <div
-              className="grow px-2 py-1.5"
-              style={{ textOverflow: 'ellipsis', wordBreak: 'break-all', overflow: 'hidden' }}
-            >
-              {currentTool.metadata.name}
-            </div>
-          </div>
-
-          <OGDialogTrigger asChild>
-            <button
-              type="button"
-              className={cn(
-                'flex h-7 w-7 items-center justify-center rounded transition-all duration-200',
-                'hover:bg-gray-200 dark:hover:bg-gray-700',
-                'focus:outline-none focus:ring-2 focus:ring-ring focus:ring-offset-1',
-                'focus:opacity-100',
-                isHovering || isFocused ? 'opacity-100' : 'pointer-events-none opacity-0',
-              )}
-              aria-label={`Delete ${currentTool.metadata.name}`}
-              tabIndex={0}
-              onFocus={() => setIsFocused(true)}
-            >
-              <TrashIcon className="h-4 w-4" />
-            </button>
-          </OGDialogTrigger>
-        </div>
-        <OGDialogTemplate
-          showCloseButton={false}
-          title={localize('com_ui_delete_tool')}
-          mainClassName="px-0"
-          className="max-w-[450px]"
-          main={
-            <Label className="text-left text-sm font-medium">
-              {localize('com_ui_delete_tool_confirm')}
-            </Label>
-          }
-          selection={{
-            selectHandler: () => removeTool(currentTool.tool_id),
-            selectClasses:
-              'bg-red-700 dark:bg-red-600 hover:bg-red-800 dark:hover:bg-red-800 transition-color duration-200 text-white',
-            selectText: localize('com_ui_delete'),
-          }}
-        />
-      </OGDialog>
-    );
-  }
-
-  // Group tool with accordion
   return (
     <OGDialog>
-      <Accordion type="single" value={accordionValue} onValueChange={setAccordionValue} collapsible>
-        <AccordionItem value={currentTool.tool_id} className="group relative w-full border-none">
-          <div
-            className="relative flex w-full items-center gap-1 rounded-lg p-1 hover:bg-gray-50 dark:hover:bg-gray-800/50"
-            onMouseEnter={() => setIsHovering(true)}
-            onMouseLeave={() => setIsHovering(false)}
-            onFocus={() => setIsFocused(true)}
-            onBlur={(e) => {
-              // Check if focus is moving to a child element
-              if (!e.currentTarget.contains(e.relatedTarget)) {
-                setIsFocused(false);
-              }
-            }}
-          >
-            <AccordionPrimitive.Header asChild>
-              <AccordionPrimitive.Trigger asChild>
-                <button
-                  type="button"
-                  className={cn(
-                    'flex grow items-center gap-1 rounded bg-transparent p-0 text-left transition-colors',
-                    'focus:outline-none focus:ring-2 focus:ring-ring focus:ring-offset-1',
-                  )}
-                >
-                  {currentTool.metadata.icon && (
-                    <div className="flex h-8 w-8 items-center justify-center overflow-hidden rounded-full">
-                      <div
-                        className="flex h-6 w-6 items-center justify-center overflow-hidden rounded-full bg-center bg-no-repeat dark:bg-white/20"
-                        style={{
-                          backgroundImage: `url(${currentTool.metadata.icon})`,
-                          backgroundSize: 'cover',
-                        }}
-                      />
-                    </div>
-                  )}
-                  <div
-                    className="grow px-2 py-1.5"
-                    style={{ textOverflow: 'ellipsis', wordBreak: 'break-all', overflow: 'hidden' }}
-                  >
-                    {currentTool.metadata.name}
-                  </div>
-                  <div className="flex items-center">
-                    {/* Container for grouped checkbox and chevron */}
-                    <div className="relative flex items-center">
-                      {/* Grouped checkbox and chevron that slide together */}
-                      <div
-                        className={cn(
-                          'flex items-center gap-2 transition-all duration-300',
-                          isHovering || isFocused ? '-translate-x-8' : 'translate-x-0',
-                        )}
-                      >
-                        <div
-                          data-checkbox-container
-                          onClick={(e) => e.stopPropagation()}
-                          className="mt-1"
-                        >
-                          <Checkbox
-                            id={`select-all-${currentTool.tool_id}`}
-                            checked={selectedTools.length === currentTool.tools?.length}
-                            onCheckedChange={(checked) => {
-                              if (currentTool.tools) {
-                                const newSelectedTools = checked
-                                  ? currentTool.tools.map((t) => t.tool_id)
-                                  : [];
-                                updateFormTools(newSelectedTools);
-                              }
-                            }}
-                            className={cn(
-                              'h-4 w-4 rounded border border-gray-300 transition-all duration-200 hover:border-gray-400 dark:border-gray-600 dark:hover:border-gray-500',
-                              isExpanded ? 'visible' : 'pointer-events-none invisible',
-                            )}
-                            onClick={(e) => e.stopPropagation()}
-                            onKeyDown={(e) => {
-                              if (e.key === 'Enter' || e.key === ' ') {
-                                e.preventDefault();
-                                e.stopPropagation();
-                                const checkbox = e.currentTarget as HTMLButtonElement;
-                                checkbox.click();
-                              }
-                            }}
-                            tabIndex={isExpanded ? 0 : -1}
-                          />
-                        </div>
-
-                        <div
-                          className={cn(
-                            'pointer-events-none flex h-4 w-4 items-center justify-center transition-transform duration-300',
-                            isExpanded ? 'rotate-180' : '',
-                          )}
-                          aria-hidden="true"
-                        >
-                          <ChevronDown className="h-4 w-4" />
-                        </div>
-                      </div>
-
-                      {/* Delete button slides in from behind */}
-                      <div
-                        className={cn(
-                          'absolute right-0 transition-all duration-300',
-                          isHovering || isFocused
-                            ? 'translate-x-0 opacity-100'
-                            : 'translate-x-8 opacity-0',
-                        )}
-                      >
-                        <OGDialogTrigger asChild>
-                          <button
-                            type="button"
-                            className={cn(
-                              'flex h-7 w-7 items-center justify-center rounded transition-colors duration-200',
-                              'hover:bg-gray-200 dark:hover:bg-gray-700',
-                              'focus:outline-none focus:ring-2 focus:ring-ring focus:ring-offset-1',
-                              'focus:translate-x-0 focus:opacity-100',
-                            )}
-                            onClick={(e) => e.stopPropagation()}
-                            aria-label={`Delete ${currentTool.metadata.name}`}
-                            tabIndex={0}
-                            onFocus={() => setIsFocused(true)}
-                          >
-                            <TrashIcon className="h-4 w-4" />
-                          </button>
-                        </OGDialogTrigger>
-                      </div>
-                    </div>
-                  </div>
-                </button>
-              </AccordionPrimitive.Trigger>
-            </AccordionPrimitive.Header>
-          </div>
-
-          <AccordionContent className="relative ml-1 pt-1 before:absolute before:bottom-2 before:left-0 before:top-0 before:w-0.5 before:bg-border-medium">
-            <div className="space-y-1">
-              {currentTool.tools?.map((subTool) => (
-                <label
-                  key={subTool.tool_id}
-                  htmlFor={subTool.tool_id}
-                  className={cn(
-                    'border-token-border-light hover:bg-token-surface-secondary flex cursor-pointer items-center rounded-lg border p-2',
-                    'ml-2 mr-1 focus-within:ring-2 focus-within:ring-ring focus-within:ring-offset-2 focus-within:ring-offset-background',
-                  )}
-                  onClick={(e) => e.stopPropagation()}
-                  onKeyDown={(e) => {
-                    e.stopPropagation();
-                  }}
-                  onMouseEnter={() => setHoveredToolId(subTool.tool_id)}
-                  onMouseLeave={() => setHoveredToolId(null)}
-                >
-                  <Checkbox
-                    id={subTool.tool_id}
-                    checked={selectedTools.includes(subTool.tool_id)}
-                    onCheckedChange={(_checked) => {
-                      const newSelectedTools = selectedTools.includes(subTool.tool_id)
-                        ? selectedTools.filter((t) => t !== subTool.tool_id)
-                        : [...selectedTools, subTool.tool_id];
-                      updateFormTools(newSelectedTools);
-                    }}
-                    onKeyDown={(e) => {
-                      e.stopPropagation();
-                      if (e.key === 'Enter' || e.key === ' ') {
-                        e.preventDefault();
-                        const checkbox = e.currentTarget as HTMLButtonElement;
-                        checkbox.click();
-                      }
-                    }}
-                    onClick={(e) => e.stopPropagation()}
-                    className="relative float-left mr-2 inline-flex h-4 w-4 cursor-pointer rounded border border-gray-300 transition-[border-color] duration-200 hover:border-gray-400 focus:outline-none focus:ring-2 focus:ring-ring focus:ring-offset-2 focus:ring-offset-background dark:border-gray-600 dark:hover:border-gray-500"
-                  />
-                  <span className="text-token-text-primary">{subTool.metadata.name}</span>
-                  {subTool.metadata.description && (
-                    <Ariakit.HovercardProvider placement="left-start">
-                      <div className="ml-auto flex h-6 w-6 items-center justify-center">
-                        <Ariakit.HovercardAnchor
-                          render={
-                            <Ariakit.Button
-                              className={cn(
-                                'flex h-5 w-5 cursor-help items-center rounded-full text-text-secondary transition-opacity duration-200',
-                                hoveredToolId === subTool.tool_id ? 'opacity-100' : 'opacity-0',
-                              )}
-                              aria-label={localize('com_ui_tool_info')}
-                            >
-                              <CircleHelpIcon className="h-4 w-4" />
-                              <Ariakit.VisuallyHidden>
-                                {localize('com_ui_tool_info')}
-                              </Ariakit.VisuallyHidden>
-                            </Ariakit.Button>
-                          }
-                        />
-                        <Ariakit.HovercardDisclosure
-                          className="rounded-full text-text-secondary focus:outline-none focus:ring-2 focus:ring-ring"
-                          aria-label={localize('com_ui_tool_more_info')}
-                          aria-expanded={hoveredToolId === subTool.tool_id}
-                          aria-controls={`tool-description-${subTool.tool_id}`}
-                        >
-                          <Ariakit.VisuallyHidden>
-                            {localize('com_ui_tool_more_info')}
-                          </Ariakit.VisuallyHidden>
-                          <ChevronDown className="h-4 w-4" />
-                        </Ariakit.HovercardDisclosure>
-                      </div>
-                      <Ariakit.Hovercard
-                        id={`tool-description-${subTool.tool_id}`}
-                        gutter={14}
-                        shift={40}
-                        flip={false}
-                        className="z-[999] w-80 scale-95 rounded-2xl border border-border-medium bg-surface-secondary p-4 text-text-primary opacity-0 shadow-md transition-all duration-200 data-[enter]:scale-100 data-[leave]:scale-95 data-[enter]:opacity-100 data-[leave]:opacity-0"
-                        portal={true}
-                        unmountOnHide={true}
-                        role="tooltip"
-                        aria-label={subTool.metadata.description}
-                      >
-                        <div className="space-y-2">
-                          <p className="text-sm text-text-secondary">
-                            {subTool.metadata.description}
-                          </p>
-                        </div>
-                      </Ariakit.Hovercard>
-                    </Ariakit.HovercardProvider>
-                  )}
-                </label>
-              ))}
+      <div
+        className="group relative flex w-full items-center gap-1 rounded-lg p-1 text-sm hover:bg-gray-50 dark:hover:bg-gray-800/50"
+        onMouseEnter={() => setIsHovering(true)}
+        onMouseLeave={() => setIsHovering(false)}
+        onFocus={() => setIsFocused(true)}
+        onBlur={(e) => {
+          // Check if focus is moving to a child element
+          if (!e.currentTarget.contains(e.relatedTarget)) {
+            setIsFocused(false);
+          }
+        }}
+      >
+        <div className="flex grow items-center">
+          {currentTool.icon && (
+            <div className="flex h-8 w-8 items-center justify-center overflow-hidden rounded-full">
+              <div
+                className="flex h-6 w-6 items-center justify-center overflow-hidden rounded-full bg-center bg-no-repeat dark:bg-white/20"
+                style={{
+                  backgroundImage: `url(${currentTool.icon})`,
+                  backgroundSize: 'cover',
+                }}
+              />
             </div>
-          </AccordionContent>
-        </AccordionItem>
-      </Accordion>
+          )}
+          <div
+            className="grow px-2 py-1.5"
+            style={{ textOverflow: 'ellipsis', wordBreak: 'break-all', overflow: 'hidden' }}
+          >
+            {currentTool.name}
+          </div>
+        </div>
+
+        <OGDialogTrigger asChild>
+          <button
+            type="button"
+            className={cn(
+              'flex h-7 w-7 items-center justify-center rounded transition-all duration-200',
+              'hover:bg-gray-200 dark:hover:bg-gray-700',
+              'focus:outline-none focus:ring-2 focus:ring-ring focus:ring-offset-1',
+              'focus:opacity-100',
+              isHovering || isFocused ? 'opacity-100' : 'pointer-events-none opacity-0',
+            )}
+            aria-label={`Delete ${currentTool.name}`}
+            tabIndex={0}
+            onFocus={() => setIsFocused(true)}
+          >
+            <TrashIcon className="h-4 w-4" />
+          </button>
+        </OGDialogTrigger>
+      </div>
       <OGDialogTemplate
         showCloseButton={false}
         title={localize('com_ui_delete_tool')}
-        mainClassName="px-0"
         className="max-w-[450px]"
         main={
-          <Label className="text-left text-sm font-medium">
-            {localize('com_ui_delete_tool_confirm')}
-          </Label>
+          <>
+            <div className="flex w-full flex-col items-start gap-2 text-sm text-text-secondary">
+              <p>
+                {localize('com_ui_delete_tool_confirm')}{' '}
+                <strong>&quot;{currentTool.name}&quot;</strong>?
+              </p>
+              {currentTool.description && (
+                <div className="flex items-start gap-2">
+                  <CircleHelpIcon className="h-4 w-4 flex-shrink-0 text-text-secondary" />
+                  <p className="text-sm">{currentTool.description}</p>
+                </div>
+              )}
+            </div>
+          </>
         }
         selection={{
-          selectHandler: () => removeTool(currentTool.tool_id),
+          selectHandler: () => removeTool(tool),
           selectClasses:
-            'bg-red-700 dark:bg-red-600 hover:bg-red-800 dark:hover:bg-red-800 transition-color duration-200 text-white',
+            'bg-red-700 hover:bg-red-800 dark:bg-red-600 dark:hover:bg-red-800 text-white',
           selectText: localize('com_ui_delete'),
         }}
       />
diff --git a/client/src/components/SidePanel/MCP/MCPPanel.tsx b/client/src/components/SidePanel/MCP/MCPPanel.tsx
index adcb81e0e..5bb6d18b8 100644
--- a/client/src/components/SidePanel/MCP/MCPPanel.tsx
+++ b/client/src/components/SidePanel/MCP/MCPPanel.tsx
@@ -56,7 +56,7 @@ function MCPPanelContent() {
       showToast({ message: localize('com_nav_mcp_vars_updated'), status: 'success' });
 
       await Promise.all([
-        queryClient.refetchQueries([QueryKeys.tools]),
+        queryClient.refetchQueries([QueryKeys.mcpTools]),
         queryClient.refetchQueries([QueryKeys.mcpAuthValues]),
         queryClient.refetchQueries([QueryKeys.mcpConnectionStatus]),
       ]);
diff --git a/client/src/components/Tools/MCPToolSelectDialog.tsx b/client/src/components/Tools/MCPToolSelectDialog.tsx
index 268cd3864..62710d032 100644
--- a/client/src/components/Tools/MCPToolSelectDialog.tsx
+++ b/client/src/components/Tools/MCPToolSelectDialog.tsx
@@ -7,8 +7,8 @@ import { useUpdateUserPluginsMutation } from 'librechat-data-provider/react-quer
 import type { TError, AgentToolType } from 'librechat-data-provider';
 import type { AgentForm, TPluginStoreDialogProps } from '~/common';
 import { useLocalize, usePluginDialogHelpers, useMCPServerManager } from '~/hooks';
-import { useGetStartupConfig, useAvailableToolsQuery } from '~/data-provider';
 import CustomUserVarsSection from '~/components/MCP/CustomUserVarsSection';
+import { useGetStartupConfig, useMCPToolsQuery } from '~/data-provider';
 import { PluginPagination } from '~/components/Plugins/Store';
 import { useAgentPanelContext } from '~/Providers';
 import MCPToolItem from './MCPToolItem';
@@ -27,8 +27,8 @@ function MCPToolSelectDialog({
   const { mcpServersMap } = useAgentPanelContext();
   const { initializeServer } = useMCPServerManager();
   const { data: startupConfig } = useGetStartupConfig();
+  const { refetch: refetchMCPTools } = useMCPToolsQuery();
   const { getValues, setValue } = useFormContext<AgentForm>();
-  const { refetch: refetchAvailableTools } = useAvailableToolsQuery(EModelEndpoint.agents);
 
   const [isInitializing, setIsInitializing] = useState<string | null>(null);
   const [configuringServer, setConfiguringServer] = useState<string | null>(null);
@@ -90,15 +90,15 @@ function MCPToolSelectDialog({
             setIsInitializing(null);
           },
           onSuccess: async () => {
-            const { data: updatedAvailableTools } = await refetchAvailableTools();
+            const { data: updatedMCPTools } = await refetchMCPTools();
 
             const currentTools = getValues('tools') || [];
             const toolsToAdd: string[] = [
               `${Constants.mcp_server}${Constants.mcp_delimiter}${serverName}`,
             ];
 
-            if (updatedAvailableTools) {
-              updatedAvailableTools.forEach((tool) => {
+            if (updatedMCPTools) {
+              updatedMCPTools.forEach((tool) => {
                 if (tool.pluginKey.endsWith(`${Constants.mcp_delimiter}${serverName}`)) {
                   toolsToAdd.push(tool.pluginKey);
                 }
diff --git a/client/src/components/Tools/ToolSelectDialog.tsx b/client/src/components/Tools/ToolSelectDialog.tsx
index cdd70b907..14bab5060 100644
--- a/client/src/components/Tools/ToolSelectDialog.tsx
+++ b/client/src/components/Tools/ToolSelectDialog.tsx
@@ -8,7 +8,7 @@ import type {
   AssistantsEndpoint,
   EModelEndpoint,
   TPluginAction,
-  AgentToolType,
+  TPlugin,
   TError,
 } from 'librechat-data-provider';
 import type { AgentForm, TPluginStoreDialogProps } from '~/common';
@@ -27,7 +27,8 @@ function ToolSelectDialog({
   const localize = useLocalize();
   const isAgentTools = isAgentsEndpoint(endpoint);
   const { getValues, setValue } = useFormContext<AgentForm>();
-  const { groupedTools, pluginTools } = useAgentPanelContext();
+  // Only use regular tools, not MCP tools
+  const { regularTools } = useAgentPanelContext();
 
   const {
     maxPage,
@@ -68,19 +69,8 @@ function ToolSelectDialog({
   const handleInstall = (pluginAction: TPluginAction) => {
     const addFunction = () => {
       const installedToolIds: string[] = getValues('tools') || [];
-      // Add the parent
       installedToolIds.push(pluginAction.pluginKey);
-
-      // If this tool is a group, add subtools too
-      const groupObj = groupedTools?.[pluginAction.pluginKey];
-      if (groupObj?.tools && groupObj.tools.length > 0) {
-        for (const sub of groupObj.tools) {
-          if (!installedToolIds.includes(sub.tool_id)) {
-            installedToolIds.push(sub.tool_id);
-          }
-        }
-      }
-      setValue('tools', Array.from(new Set(installedToolIds))); // no duplicates just in case
+      setValue('tools', Array.from(new Set(installedToolIds)));
     };
 
     if (!pluginAction.auth) {
@@ -98,19 +88,12 @@ function ToolSelectDialog({
   };
 
   const onRemoveTool = (toolId: string) => {
-    const groupObj = groupedTools?.[toolId];
-    const toolIdsToRemove = [toolId];
-    if (groupObj?.tools && groupObj.tools.length > 0) {
-      toolIdsToRemove.push(...groupObj.tools.map((sub) => sub.tool_id));
-    }
-    // Remove these from the formTools
     updateUserPlugins.mutate(
       { pluginKey: toolId, action: 'uninstall', auth: {}, isEntityTool: true },
       {
         onError: (error: unknown) => handleInstallError(error as TError),
         onSuccess: () => {
-          const remainingToolIds =
-            getValues('tools')?.filter((toolId) => !toolIdsToRemove.includes(toolId)) || [];
+          const remainingToolIds = getValues('tools')?.filter((id) => id !== toolId) || [];
           setValue('tools', remainingToolIds);
         },
       },
@@ -119,7 +102,8 @@ function ToolSelectDialog({
 
   const onAddTool = (pluginKey: string) => {
     setShowPluginAuthForm(false);
-    const availablePluginFromKey = pluginTools?.find((p) => p.pluginKey === pluginKey);
+    // Find the tool in regularTools
+    const availablePluginFromKey = regularTools?.find((p) => p.pluginKey === pluginKey);
     setSelectedPlugin(availablePluginFromKey);
 
     const { authConfig, authenticated = false } = availablePluginFromKey ?? {};
@@ -134,30 +118,19 @@ function ToolSelectDialog({
     }
   };
 
-  const filteredTools = Object.values(groupedTools || {}).filter(
-    (currentTool: AgentToolType & { tools?: AgentToolType[] }) => {
-      if (currentTool.metadata?.name?.toLowerCase().includes(searchValue.toLowerCase())) {
-        return true;
-      }
-      if (currentTool.tools) {
-        return currentTool.tools.some((childTool) =>
-          childTool.metadata?.name?.toLowerCase().includes(searchValue.toLowerCase()),
-        );
-      }
-      return false;
-    },
-  );
+  const filteredTools = (regularTools || []).filter((tool: TPlugin) => {
+    return tool.name?.toLowerCase().includes(searchValue.toLowerCase());
+  });
 
   useEffect(() => {
     if (filteredTools) {
-      setMaxPage(Math.ceil(Object.keys(filteredTools || {}).length / itemsPerPage));
+      setMaxPage(Math.ceil(filteredTools.length / itemsPerPage));
       if (searchChanged) {
         setCurrentPage(1);
         setSearchChanged(false);
       }
     }
   }, [
-    pluginTools,
     searchValue,
     itemsPerPage,
     filteredTools,
@@ -254,10 +227,13 @@ function ToolSelectDialog({
                     .map((tool, index) => (
                       <ToolItem
                         key={index}
-                        tool={tool}
-                        isInstalled={getValues('tools')?.includes(tool.tool_id) || false}
-                        onAddTool={() => onAddTool(tool.tool_id)}
-                        onRemoveTool={() => onRemoveTool(tool.tool_id)}
+                        tool={{
+                          tool_id: tool.pluginKey,
+                          metadata: tool,
+                        }}
+                        isInstalled={getValues('tools')?.includes(tool.pluginKey) || false}
+                        onAddTool={() => onAddTool(tool.pluginKey)}
+                        onRemoveTool={() => onRemoveTool(tool.pluginKey)}
                       />
                     ))}
               </div>
diff --git a/client/src/data-provider/index.ts b/client/src/data-provider/index.ts
index 1b1ceed19..1e2582cb8 100644
--- a/client/src/data-provider/index.ts
+++ b/client/src/data-provider/index.ts
@@ -11,5 +11,6 @@ export * from './connection';
 export * from './mutations';
 export * from './prompts';
 export * from './queries';
+export * from './mcp';
 export * from './roles';
 export * from './tags';
diff --git a/client/src/data-provider/mcp.ts b/client/src/data-provider/mcp.ts
new file mode 100644
index 000000000..cc144f78b
--- /dev/null
+++ b/client/src/data-provider/mcp.ts
@@ -0,0 +1,29 @@
+/**
+ * Dedicated queries for MCP (Model Context Protocol) tools
+ * Decoupled from regular LibreChat tools
+ */
+import { useQuery } from '@tanstack/react-query';
+import { QueryKeys, dataService } from 'librechat-data-provider';
+import type { UseQueryOptions, QueryObserverResult } from '@tanstack/react-query';
+import type { TPlugin } from 'librechat-data-provider';
+
+/**
+ * Hook for fetching MCP-specific tools
+ * @param config - React Query configuration
+ * @returns MCP tools grouped by server
+ */
+export const useMCPToolsQuery = <TData = TPlugin[]>(
+  config?: UseQueryOptions<TPlugin[], unknown, TData>,
+): QueryObserverResult<TData> => {
+  return useQuery<TPlugin[], unknown, TData>(
+    [QueryKeys.mcpTools],
+    () => dataService.getMCPTools(),
+    {
+      refetchOnWindowFocus: false,
+      refetchOnReconnect: false,
+      refetchOnMount: false,
+      staleTime: 5 * 60 * 1000, // 5 minutes
+      ...config,
+    },
+  );
+};
diff --git a/client/src/data-provider/queries.ts b/client/src/data-provider/queries.ts
index 447775067..8f2b702a3 100644
--- a/client/src/data-provider/queries.ts
+++ b/client/src/data-provider/queries.ts
@@ -178,7 +178,8 @@ export const useConversationTagsQuery = (
  */
 
 /**
- * Hook for getting all available tools for Assistants
+ * Hook for getting available LibreChat tools (excludes MCP tools)
+ * For MCP tools, use `useMCPToolsQuery` from mcp-queries.ts
  */
 export const useAvailableToolsQuery = <TData = t.TPlugin[]>(
   endpoint: t.AssistantsEndpoint | EModelEndpoint.agents,
diff --git a/client/src/hooks/MCP/useGetMCPTools.ts b/client/src/hooks/MCP/useGetMCPTools.ts
index adffb963e..2785675b9 100644
--- a/client/src/hooks/MCP/useGetMCPTools.ts
+++ b/client/src/hooks/MCP/useGetMCPTools.ts
@@ -1,32 +1,37 @@
 import { useMemo } from 'react';
-import { Constants, EModelEndpoint } from 'librechat-data-provider';
+import { Constants } from 'librechat-data-provider';
 import type { TPlugin } from 'librechat-data-provider';
-import { useAvailableToolsQuery, useGetStartupConfig } from '~/data-provider';
+import { useMCPToolsQuery, useGetStartupConfig } from '~/data-provider';
 
+/**
+ * Hook for fetching and filtering MCP tools based on server configuration
+ * Uses the dedicated MCP tools query instead of filtering from general tools
+ */
 export function useGetMCPTools() {
   const { data: startupConfig } = useGetStartupConfig();
-  const { data: rawMcpTools } = useAvailableToolsQuery(EModelEndpoint.agents, {
+
+  // Use dedicated MCP tools query
+  const { data: rawMcpTools } = useMCPToolsQuery({
     select: (data: TPlugin[]) => {
+      // Group tools by server for easier management
       const mcpToolsMap = new Map<string, TPlugin>();
       data.forEach((tool) => {
-        const isMCP = tool.pluginKey.includes(Constants.mcp_delimiter);
-        if (isMCP) {
-          const parts = tool.pluginKey.split(Constants.mcp_delimiter);
-          const serverName = parts[parts.length - 1];
-          if (!mcpToolsMap.has(serverName)) {
-            mcpToolsMap.set(serverName, {
-              name: serverName,
-              pluginKey: tool.pluginKey,
-              authConfig: tool.authConfig,
-              authenticated: tool.authenticated,
-            });
-          }
+        const parts = tool.pluginKey.split(Constants.mcp_delimiter);
+        const serverName = parts[parts.length - 1];
+        if (!mcpToolsMap.has(serverName)) {
+          mcpToolsMap.set(serverName, {
+            name: serverName,
+            pluginKey: tool.pluginKey,
+            authConfig: tool.authConfig,
+            authenticated: tool.authenticated,
+          });
         }
       });
       return Array.from(mcpToolsMap.values());
     },
   });
 
+  // Filter out servers that have chatMenu disabled
   const mcpToolDetails = useMemo(() => {
     if (!rawMcpTools || !startupConfig?.mcpServers) {
       return rawMcpTools;
diff --git a/client/src/hooks/MCP/useMCPServerManager.ts b/client/src/hooks/MCP/useMCPServerManager.ts
index 733168c1a..c30193919 100644
--- a/client/src/hooks/MCP/useMCPServerManager.ts
+++ b/client/src/hooks/MCP/useMCPServerManager.ts
@@ -53,7 +53,7 @@ export function useMCPServerManager({ conversationId }: { conversationId?: strin
       showToast({ message: localize('com_nav_mcp_vars_updated'), status: 'success' });
 
       await Promise.all([
-        queryClient.refetchQueries([QueryKeys.tools]),
+        queryClient.refetchQueries([QueryKeys.mcpTools]),
         queryClient.refetchQueries([QueryKeys.mcpAuthValues]),
         queryClient.refetchQueries([QueryKeys.mcpConnectionStatus]),
       ]);
@@ -170,7 +170,7 @@ export function useMCPServerManager({ conversationId }: { conversationId?: strin
               setMCPValues([...currentValues, serverName]);
             }
 
-            await queryClient.invalidateQueries([QueryKeys.tools]);
+            await queryClient.invalidateQueries([QueryKeys.mcpTools]);
 
             // This delay is to ensure UI has updated with new connection status before cleanup
             // Otherwise servers will show as disconnected for a second after OAuth flow completes
diff --git a/client/src/hooks/MCP/useVisibleTools.ts b/client/src/hooks/MCP/useVisibleTools.ts
index acb48bf11..1e48d0891 100644
--- a/client/src/hooks/MCP/useVisibleTools.ts
+++ b/client/src/hooks/MCP/useVisibleTools.ts
@@ -1,79 +1,52 @@
 import { useMemo } from 'react';
 import { Constants } from 'librechat-data-provider';
-import type { AgentToolType } from 'librechat-data-provider';
+import type { TPlugin } from 'librechat-data-provider';
 import type { MCPServerInfo } from '~/common';
 
-type GroupedToolType = AgentToolType & { tools?: AgentToolType[] };
-type GroupedToolsRecord = Record<string, GroupedToolType>;
-
 interface VisibleToolsResult {
   toolIds: string[];
   mcpServerNames: string[];
 }
 
 /**
- * Custom hook to calculate visible tool IDs based on selected tools and their parent groups.
- * If any subtool of a group is selected, the parent group tool is also made visible.
+ * Custom hook to calculate visible tool IDs based on selected tools.
+ * Separates regular LibreChat tools from MCP servers.
  *
  * @param selectedToolIds - Array of selected tool IDs
- * @param allTools - Record of all available tools
+ * @param regularTools - Array of regular LibreChat tools
  * @param mcpServersMap - Map of all MCP servers
  * @returns Object containing separate arrays of visible tool IDs for regular and MCP tools
  */
 export function useVisibleTools(
   selectedToolIds: string[] | undefined,
-  allTools: GroupedToolsRecord | undefined,
+  regularTools: TPlugin[] | undefined,
   mcpServersMap: Map<string, MCPServerInfo>,
 ): VisibleToolsResult {
   return useMemo(() => {
     const mcpServers = new Set<string>();
-    const selectedSet = new Set<string>();
-    const regularToolIds = new Set<string>();
+    const regularToolIds: string[] = [];
 
     for (const toolId of selectedToolIds ?? []) {
-      if (!toolId.includes(Constants.mcp_delimiter)) {
-        selectedSet.add(toolId);
-        continue;
-      }
-      const serverName = toolId.split(Constants.mcp_delimiter)[1];
-      if (!serverName) {
-        continue;
-      }
-      mcpServers.add(serverName);
-    }
-
-    if (allTools) {
-      for (const [toolId, toolObj] of Object.entries(allTools)) {
-        if (selectedSet.has(toolId)) {
-          regularToolIds.add(toolId);
-        }
-
-        if (toolObj.tools?.length) {
-          for (const subtool of toolObj.tools) {
-            if (selectedSet.has(subtool.tool_id)) {
-              regularToolIds.add(toolId);
-              break;
-            }
-          }
+      // MCP tools/servers
+      if (toolId.includes(Constants.mcp_delimiter)) {
+        const serverName = toolId.split(Constants.mcp_delimiter)[1];
+        if (serverName) {
+          mcpServers.add(serverName);
         }
       }
-    }
-
-    if (mcpServersMap) {
-      for (const [mcpServerName] of mcpServersMap) {
-        if (mcpServers.has(mcpServerName)) {
-          continue;
-        }
-        /** Legacy check */
-        if (selectedSet.has(mcpServerName)) {
-          mcpServers.add(mcpServerName);
-        }
+      // Legacy MCP server check (just server name)
+      else if (mcpServersMap.has(toolId)) {
+        mcpServers.add(toolId);
+      }
+      // Regular LibreChat tools
+      else if (regularTools?.some((t) => t.pluginKey === toolId)) {
+        regularToolIds.push(toolId);
       }
     }
 
     return {
-      toolIds: Array.from(regularToolIds).sort((a, b) => a.localeCompare(b)),
+      toolIds: regularToolIds.sort((a, b) => a.localeCompare(b)),
       mcpServerNames: Array.from(mcpServers).sort((a, b) => a.localeCompare(b)),
     };
-  }, [allTools, mcpServersMap, selectedToolIds]);
+  }, [regularTools, mcpServersMap, selectedToolIds]);
 }
diff --git a/packages/data-provider/src/api-endpoints.ts b/packages/data-provider/src/api-endpoints.ts
index be3f2a62a..8c1447abe 100644
--- a/packages/data-provider/src/api-endpoints.ts
+++ b/packages/data-provider/src/api-endpoints.ts
@@ -222,6 +222,10 @@ export const agents = ({ path = '', options }: { path?: string; options?: object
   return url;
 };
 
+export const mcp = {
+  tools: `${BASE_URL}/api/mcp/tools`,
+};
+
 export const revertAgentVersion = (agent_id: string) => `${agents({ path: `${agent_id}/revert` })}`;
 
 export const files = () => `${BASE_URL}/api/files`;
diff --git a/packages/data-provider/src/data-service.ts b/packages/data-provider/src/data-service.ts
index 7116f0d7c..9926e18be 100644
--- a/packages/data-provider/src/data-service.ts
+++ b/packages/data-provider/src/data-service.ts
@@ -297,6 +297,12 @@ export const getAvailableTools = (
   return request.get(path);
 };
 
+/* MCP Tools - Decoupled from regular tools */
+
+export const getMCPTools = (): Promise<s.TPlugin[]> => {
+  return request.get(endpoints.mcp.tools);
+};
+
 export const getVerifyAgentToolAuth = (
   params: q.VerifyToolAuthParams,
 ): Promise<q.VerifyToolAuthResponse> => {
diff --git a/packages/data-provider/src/keys.ts b/packages/data-provider/src/keys.ts
index 79d1fa38d..1d6e1d813 100644
--- a/packages/data-provider/src/keys.ts
+++ b/packages/data-provider/src/keys.ts
@@ -26,6 +26,7 @@ export enum QueryKeys {
   tools = 'tools',
   toolAuth = 'toolAuth',
   toolCalls = 'toolCalls',
+  mcpTools = 'mcpTools',
   mcpConnectionStatus = 'mcpConnectionStatus',
   mcpAuthValues = 'mcpAuthValues',
   agentTools = 'agentTools',
diff --git a/packages/data-provider/src/react-query/react-query-service.ts b/packages/data-provider/src/react-query/react-query-service.ts
index ab150a133..db1f0c905 100644
--- a/packages/data-provider/src/react-query/react-query-service.ts
+++ b/packages/data-provider/src/react-query/react-query-service.ts
@@ -147,6 +147,7 @@ export const useRevokeUserKeyMutation = (name: string): UseMutationResult<unknow
         queryClient.invalidateQueries([QueryKeys.assistantDocs]);
         queryClient.invalidateQueries([QueryKeys.assistants]);
         queryClient.invalidateQueries([QueryKeys.assistant]);
+        queryClient.invalidateQueries([QueryKeys.mcpTools]);
         queryClient.invalidateQueries([QueryKeys.actions]);
         queryClient.invalidateQueries([QueryKeys.tools]);
       }
@@ -172,6 +173,7 @@ export const useRevokeAllUserKeysMutation = (): UseMutationResult<unknown> => {
       queryClient.invalidateQueries([QueryKeys.assistantDocs]);
       queryClient.invalidateQueries([QueryKeys.assistants]);
       queryClient.invalidateQueries([QueryKeys.assistant]);
+      queryClient.invalidateQueries([QueryKeys.mcpTools]);
       queryClient.invalidateQueries([QueryKeys.actions]);
       queryClient.invalidateQueries([QueryKeys.tools]);
     },
@@ -337,7 +339,7 @@ export const useReinitializeMCPServerMutation = (): UseMutationResult<
   const queryClient = useQueryClient();
   return useMutation((serverName: string) => dataService.reinitializeMCPServer(serverName), {
     onSuccess: () => {
-      queryClient.refetchQueries([QueryKeys.tools]);
+      queryClient.refetchQueries([QueryKeys.mcpTools]);
     },
   });
 };