diff --git a/api/server/services/MCP.js b/api/server/services/MCP.js
index 791f824dbf..162e02d91e 100644
--- a/api/server/services/MCP.js
+++ b/api/server/services/MCP.js
@@ -442,10 +442,10 @@ async function getMCPSetupData(userId) {
   }
 
   const mcpManager = getMCPManager(userId);
-  /** @type {ReturnType<MCPManager['getAllConnections']>} */
+  /** @type {Map<string, import('@librechat/api').MCPConnection>} */
   let appConnections = new Map();
   try {
-    appConnections = (await mcpManager.getAllConnections()) || new Map();
+    appConnections = (await mcpManager.appConnections?.getAll()) || new Map();
   } catch (error) {
     logger.error(`[MCP][User: ${userId}] Error getting app connections:`, error);
   }
diff --git a/api/server/services/MCP.spec.js b/api/server/services/MCP.spec.js
index 9773d58745..8b9f7b675d 100644
--- a/api/server/services/MCP.spec.js
+++ b/api/server/services/MCP.spec.js
@@ -123,7 +123,7 @@ describe('tests for the new helper functions used by the MCP connection status e
     beforeEach(() => {
       mockGetAppConfig = require('./Config').getAppConfig;
       mockGetMCPManager.mockReturnValue({
-        getAllConnections: jest.fn(() => new Map()),
+        appConnections: { getAll: jest.fn(() => new Map()) },
         getUserConnections: jest.fn(() => new Map()),
         getOAuthServers: jest.fn(() => new Set()),
       });
@@ -137,7 +137,7 @@ describe('tests for the new helper functions used by the MCP connection status e
       const mockOAuthServers = new Set(['server2']);
 
       const mockMCPManager = {
-        getAllConnections: jest.fn(() => mockAppConnections),
+        appConnections: { getAll: jest.fn(() => mockAppConnections) },
         getUserConnections: jest.fn(() => mockUserConnections),
         getOAuthServers: jest.fn(() => mockOAuthServers),
       };
@@ -147,7 +147,7 @@ describe('tests for the new helper functions used by the MCP connection status e
 
       expect(mockGetAppConfig).toHaveBeenCalled();
       expect(mockGetMCPManager).toHaveBeenCalledWith(mockUserId);
-      expect(mockMCPManager.getAllConnections).toHaveBeenCalled();
+      expect(mockMCPManager.appConnections.getAll).toHaveBeenCalled();
       expect(mockMCPManager.getUserConnections).toHaveBeenCalledWith(mockUserId);
       expect(mockMCPManager.getOAuthServers).toHaveBeenCalled();
 
@@ -168,7 +168,7 @@ describe('tests for the new helper functions used by the MCP connection status e
       mockGetAppConfig.mockResolvedValue({ mcpConfig: mockConfig.mcpServers });
 
       const mockMCPManager = {
-        getAllConnections: jest.fn(() => null),
+        appConnections: { getAll: jest.fn(() => null) },
         getUserConnections: jest.fn(() => null),
         getOAuthServers: jest.fn(() => null),
       };
diff --git a/api/server/services/Tools/mcp.js b/api/server/services/Tools/mcp.js
index 2669ba4658..e6d293800d 100644
--- a/api/server/services/Tools/mcp.js
+++ b/api/server/services/Tools/mcp.js
@@ -29,7 +29,7 @@ async function reinitMCPServer({
   flowManager: _flowManager,
 }) {
   /** @type {MCPConnection | null} */
-  let userConnection = null;
+  let connection = null;
   /** @type {LCAvailableTools | null} */
   let availableTools = null;
   /** @type {ReturnType<MCPConnection['fetchTools']> | null} */
@@ -50,7 +50,7 @@ async function reinitMCPServer({
       });
 
     try {
-      userConnection = await mcpManager.getUserConnection({
+      connection = await mcpManager.getConnection({
         user,
         signal,
         forceNew,
@@ -70,7 +70,7 @@ async function reinitMCPServer({
 
       logger.info(`[MCP Reinitialize] Successfully established connection for ${serverName}`);
     } catch (err) {
-      logger.info(`[MCP Reinitialize] getUserConnection threw error: ${err.message}`);
+      logger.info(`[MCP Reinitialize] getConnection threw error: ${err.message}`);
       logger.info(
         `[MCP Reinitialize] OAuth state - oauthRequired: ${oauthRequired}, oauthUrl: ${oauthUrl ? 'present' : 'null'}`,
       );
@@ -95,8 +95,8 @@ async function reinitMCPServer({
       }
     }
 
-    if (userConnection && !oauthRequired) {
-      tools = await userConnection.fetchTools();
+    if (connection && !oauthRequired) {
+      tools = await connection.fetchTools();
       availableTools = await updateMCPServerTools({
         serverName,
         tools,
@@ -111,7 +111,7 @@ async function reinitMCPServer({
       if (oauthRequired) {
         return `MCP server '${serverName}' ready for OAuth authentication`;
       }
-      if (userConnection) {
+      if (connection) {
         return `MCP server '${serverName}' reinitialized successfully`;
       }
       return `Failed to reinitialize MCP server '${serverName}'`;
@@ -119,7 +119,7 @@ async function reinitMCPServer({
 
     const result = {
       availableTools,
-      success: Boolean((userConnection && !oauthRequired) || (oauthRequired && oauthUrl)),
+      success: Boolean((connection && !oauthRequired) || (oauthRequired && oauthUrl)),
       message: getResponseMessage(),
       oauthRequired,
       serverName,
diff --git a/packages/api/src/mcp/MCPManager.ts b/packages/api/src/mcp/MCPManager.ts
index d25f652b40..9d3145c632 100644
--- a/packages/api/src/mcp/MCPManager.ts
+++ b/packages/api/src/mcp/MCPManager.ts
@@ -20,8 +20,6 @@ import { processMCPEnv } from '~/utils/env';
  */
 export class MCPManager extends UserConnectionManager {
   private static instance: MCPManager | null;
-  // Connections shared by all users.
-  private appConnections: ConnectionsRepository | null = null;
 
   /** Creates and initializes the singleton MCPManager instance */
   public static async createInstance(configs: t.MCPServers): Promise<MCPManager> {
@@ -43,9 +41,25 @@ export class MCPManager extends UserConnectionManager {
     this.appConnections = new ConnectionsRepository(this.serversRegistry.appServerConfigs!);
   }
 
-  /** Returns all app-level connections */
-  public async getAllConnections(): Promise<Map<string, MCPConnection> | null> {
-    return this.appConnections!.getAll();
+  /** Retrieves an app-level or user-specific connection based on provided arguments */
+  public async getConnection(
+    args: {
+      serverName: string;
+      user?: TUser;
+      forceNew?: boolean;
+      flowManager?: FlowStateManager<MCPOAuthTokens | null>;
+    } & Omit<t.OAuthConnectionOptions, 'useOAuth' | 'user' | 'flowManager'>,
+  ): Promise<MCPConnection> {
+    if (this.appConnections!.has(args.serverName)) {
+      return this.appConnections!.get(args.serverName);
+    } else if (args.user?.id) {
+      return this.getUserConnection(args as Parameters<typeof this.getUserConnection>[0]);
+    } else {
+      throw new McpError(
+        ErrorCode.InvalidRequest,
+        `No connection found for server ${args.serverName}`,
+      );
+    }
   }
 
   /** Get servers that require OAuth */
@@ -180,30 +194,19 @@ Please follow these instructions when using tools from the respective MCP server
     const logPrefix = userId ? `[MCP][User: ${userId}][${serverName}]` : `[MCP][${serverName}]`;
 
     try {
-      if (!this.appConnections?.has(serverName) && userId && user) {
-        this.updateUserLastActivity(userId);
-        /** Get or create user-specific connection */
-        connection = await this.getUserConnection({
-          user,
-          serverName,
-          flowManager,
-          tokenMethods,
-          oauthStart,
-          oauthEnd,
-          signal: options?.signal,
-          customUserVars,
-          requestBody,
-        });
-      } else {
-        /** App-level connection */
-        connection = await this.appConnections!.get(serverName);
-        if (!connection) {
-          throw new McpError(
-            ErrorCode.InvalidRequest,
-            `${logPrefix} No app-level connection found. Cannot execute tool ${toolName}.`,
-          );
-        }
-      }
+      if (userId && user) this.updateUserLastActivity(userId);
+
+      connection = await this.getConnection({
+        serverName,
+        user,
+        flowManager,
+        tokenMethods,
+        oauthStart,
+        oauthEnd,
+        signal: options?.signal,
+        customUserVars,
+        requestBody,
+      });
 
       if (!(await connection.isConnected())) {
         /** May happen if getUserConnection failed silently or app connection dropped */
diff --git a/packages/api/src/mcp/UserConnectionManager.ts b/packages/api/src/mcp/UserConnectionManager.ts
index 92d6e012e7..7f5862b2a8 100644
--- a/packages/api/src/mcp/UserConnectionManager.ts
+++ b/packages/api/src/mcp/UserConnectionManager.ts
@@ -4,6 +4,7 @@ import { MCPConnectionFactory } from '~/mcp/MCPConnectionFactory';
 import { MCPServersRegistry } from '~/mcp/MCPServersRegistry';
 import { MCPConnection } from './connection';
 import type * as t from './types';
+import { ConnectionsRepository } from '~/mcp/ConnectionsRepository';
 
 /**
  * Abstract base class for managing user-specific MCP connections with lifecycle management.
@@ -14,6 +15,9 @@ import type * as t from './types';
  */
 export abstract class UserConnectionManager {
   protected readonly serversRegistry: MCPServersRegistry;
+  // Connections shared by all users.
+  public appConnections: ConnectionsRepository | null = null;
+  // Connections per userId -> serverName -> connection
   protected userConnections: Map<string, Map<string, MCPConnection>> = new Map();
   /** Last activity timestamp for users (not per server) */
   protected userLastActivity: Map<string, number> = new Map();
@@ -60,6 +64,13 @@ export abstract class UserConnectionManager {
       throw new McpError(ErrorCode.InvalidRequest, `[MCP] User object missing id property`);
     }
 
+    if (this.appConnections!.has(serverName)) {
+      throw new McpError(
+        ErrorCode.InvalidRequest,
+        `[MCP][User: ${userId}] Trying to create user-specific connection for app-level server "${serverName}"`,
+      );
+    }
+
     const userServerMap = this.userConnections.get(userId);
     let connection = forceNew ? undefined : userServerMap?.get(serverName);
     const now = Date.now();