diff --git a/packages/cli/src/commands/mcp/list.test.ts b/packages/cli/src/commands/mcp/list.test.ts
index 30d88af995..60912c51f5 100644
--- a/packages/cli/src/commands/mcp/list.test.ts
+++ b/packages/cli/src/commands/mcp/list.test.ts
@@ -32,6 +32,7 @@ vi.mock('@google/gemini-cli-core', async (importOriginal) => {
   return {
     ...original,
     createTransport: vi.fn(),
+
     MCPServerStatus: {
       CONNECTED: 'CONNECTED',
       CONNECTING: 'CONNECTING',
@@ -223,4 +224,46 @@ describe('mcp list command', () => {
       ),
     );
   });
+
+  it('should filter servers based on admin allowlist passed in settings', async () => {
+    const settingsWithAllowlist = mergeSettings({}, {}, {}, {}, true);
+    settingsWithAllowlist.admin = {
+      secureModeEnabled: false,
+      extensions: { enabled: true },
+      skills: { enabled: true },
+      mcp: {
+        enabled: true,
+        config: {
+          'allowed-server': { url: 'http://allowed' },
+        },
+      },
+    };
+
+    settingsWithAllowlist.mcpServers = {
+      'allowed-server': { command: 'cmd1' },
+      'forbidden-server': { command: 'cmd2' },
+    };
+
+    mockedLoadSettings.mockReturnValue({
+      merged: settingsWithAllowlist,
+    });
+
+    mockClient.connect.mockResolvedValue(undefined);
+    mockClient.ping.mockResolvedValue(undefined);
+
+    await listMcpServers(settingsWithAllowlist);
+
+    expect(debugLogger.log).toHaveBeenCalledWith(
+      expect.stringContaining('allowed-server'),
+    );
+    expect(debugLogger.log).not.toHaveBeenCalledWith(
+      expect.stringContaining('forbidden-server'),
+    );
+    expect(mockedCreateTransport).toHaveBeenCalledWith(
+      'allowed-server',
+      expect.objectContaining({ url: 'http://allowed' }), // Should use admin config
+      false,
+      expect.anything(),
+    );
+  });
 });
diff --git a/packages/cli/src/commands/mcp/list.ts b/packages/cli/src/commands/mcp/list.ts
index 50fc222f71..d51093fbfa 100644
--- a/packages/cli/src/commands/mcp/list.ts
+++ b/packages/cli/src/commands/mcp/list.ts
@@ -6,12 +6,14 @@
 
 // File for 'gemini mcp list' command
 import type { CommandModule } from 'yargs';
-import { loadSettings } from '../../config/settings.js';
+import { type MergedSettings, loadSettings } from '../../config/settings.js';
 import type { MCPServerConfig } from '@google/gemini-cli-core';
 import {
   MCPServerStatus,
   createTransport,
   debugLogger,
+  applyAdminAllowlist,
+  getAdminBlockedMcpServersMessage,
 } from '@google/gemini-cli-core';
 import { Client } from '@modelcontextprotocol/sdk/client/index.js';
 import { ExtensionManager } from '../../config/extension-manager.js';
@@ -24,18 +26,24 @@ const COLOR_YELLOW = '\u001b[33m';
 const COLOR_RED = '\u001b[31m';
 const RESET_COLOR = '\u001b[0m';
 
-export async function getMcpServersFromConfig(): Promise<
-  Record<string, MCPServerConfig>
-> {
-  const settings = loadSettings();
+export async function getMcpServersFromConfig(
+  settings?: MergedSettings,
+): Promise<{
+  mcpServers: Record<string, MCPServerConfig>;
+  blockedServerNames: string[];
+}> {
+  if (!settings) {
+    settings = loadSettings().merged;
+  }
+
   const extensionManager = new ExtensionManager({
-    settings: settings.merged,
+    settings,
     workspaceDir: process.cwd(),
     requestConsent: requestConsentNonInteractive,
     requestSetting: promptForSetting,
   });
   const extensions = await extensionManager.loadExtensions();
-  const mcpServers = { ...settings.merged.mcpServers };
+  const mcpServers = { ...settings.mcpServers };
   for (const extension of extensions) {
     Object.entries(extension.mcpServers || {}).forEach(([key, server]) => {
       if (mcpServers[key]) {
@@ -47,7 +55,11 @@ export async function getMcpServersFromConfig(): Promise<
       };
     });
   }
-  return mcpServers;
+
+  const adminAllowlist = settings.admin?.mcp?.config;
+  const filteredResult = applyAdminAllowlist(mcpServers, adminAllowlist);
+
+  return filteredResult;
 }
 
 async function testMCPConnection(
@@ -103,12 +115,23 @@ async function getServerStatus(
   return testMCPConnection(serverName, server);
 }
 
-export async function listMcpServers(): Promise<void> {
-  const mcpServers = await getMcpServersFromConfig();
+export async function listMcpServers(settings?: MergedSettings): Promise<void> {
+  const { mcpServers, blockedServerNames } =
+    await getMcpServersFromConfig(settings);
   const serverNames = Object.keys(mcpServers);
 
+  if (blockedServerNames.length > 0) {
+    const message = getAdminBlockedMcpServersMessage(
+      blockedServerNames,
+      undefined,
+    );
+    debugLogger.log(COLOR_YELLOW + message + RESET_COLOR + '\n');
+  }
+
   if (serverNames.length === 0) {
-    debugLogger.log('No MCP servers configured.');
+    if (blockedServerNames.length === 0) {
+      debugLogger.log('No MCP servers configured.');
+    }
     return;
   }
 
@@ -154,11 +177,15 @@ export async function listMcpServers(): Promise<void> {
   }
 }
 
-export const listCommand: CommandModule = {
+interface ListArgs {
+  settings?: MergedSettings;
+}
+
+export const listCommand: CommandModule<object, ListArgs> = {
   command: 'list',
   describe: 'List all configured MCP servers',
-  handler: async () => {
-    await listMcpServers();
+  handler: async (argv) => {
+    await listMcpServers(argv.settings);
     await exitCli();
   },
 };
diff --git a/packages/cli/src/config/config.test.ts b/packages/cli/src/config/config.test.ts
index bc1c582a23..4342675500 100644
--- a/packages/cli/src/config/config.test.ts
+++ b/packages/cli/src/config/config.test.ts
@@ -1511,7 +1511,7 @@ describe('loadCliConfig with admin.mcp.config', () => {
     });
     const config = await loadCliConfig(settings, 'test-session', argv);
 
-    const mergedServers = config.getMcpServers();
+    const mergedServers = config.getMcpServers() ?? {};
     expect(mergedServers).toHaveProperty('serverA');
     expect(mergedServers).not.toHaveProperty('serverB');
   });
@@ -1569,9 +1569,9 @@ describe('loadCliConfig with admin.mcp.config', () => {
     });
     const config = await loadCliConfig(settings, 'test-session', argv);
 
-    const mergedServers = config.getMcpServers();
+    const mergedServers = config.getMcpServers() ?? {};
     expect(mergedServers).not.toHaveProperty('serverC');
-    expect(Object.keys(mergedServers || {})).toHaveLength(0);
+    expect(Object.keys(mergedServers)).toHaveLength(0);
   });
 
   it('should merge local fields and prefer admin tool filters', async () => {
@@ -1601,7 +1601,7 @@ describe('loadCliConfig with admin.mcp.config', () => {
     });
     const config = await loadCliConfig(settings, 'test-session', argv);
 
-    const serverA = config.getMcpServers()?.['serverA'];
+    const serverA = (config.getMcpServers() ?? {})['serverA'];
     expect(serverA).toMatchObject({
       timeout: 1234,
       includeTools: ['admin_tool'],
diff --git a/packages/cli/src/config/config.ts b/packages/cli/src/config/config.ts
index f904922ba9..dec86e980c 100755
--- a/packages/cli/src/config/config.ts
+++ b/packages/cli/src/config/config.ts
@@ -36,9 +36,10 @@ import {
   GEMINI_MODEL_ALIAS_AUTO,
   getAdminErrorMessage,
   Config,
+  applyAdminAllowlist,
+  getAdminBlockedMcpServersMessage,
 } from '@google/gemini-cli-core';
 import type {
-  MCPServerConfig,
   HookDefinition,
   HookEventName,
   OutputFormat,
@@ -692,38 +693,17 @@ export async function loadCliConfig(
   let mcpServers = mcpEnabled ? settings.mcpServers : {};
 
   if (mcpEnabled && adminAllowlist && Object.keys(adminAllowlist).length > 0) {
-    const filteredMcpServers: Record<string, MCPServerConfig> = {};
-    for (const [serverId, localConfig] of Object.entries(mcpServers)) {
-      const adminConfig = adminAllowlist[serverId];
-      if (adminConfig) {
-        const mergedConfig = {
-          ...localConfig,
-          url: adminConfig.url,
-          type: adminConfig.type,
-          trust: adminConfig.trust,
-        };
-
-        // Remove local connection details
-        delete mergedConfig.command;
-        delete mergedConfig.args;
-        delete mergedConfig.env;
-        delete mergedConfig.cwd;
-        delete mergedConfig.httpUrl;
-        delete mergedConfig.tcp;
-
-        if (
-          (adminConfig.includeTools && adminConfig.includeTools.length > 0) ||
-          (adminConfig.excludeTools && adminConfig.excludeTools.length > 0)
-        ) {
-          mergedConfig.includeTools = adminConfig.includeTools;
-          mergedConfig.excludeTools = adminConfig.excludeTools;
-        }
-
-        filteredMcpServers[serverId] = mergedConfig;
-      }
-    }
-    mcpServers = filteredMcpServers;
+    const result = applyAdminAllowlist(mcpServers, adminAllowlist);
+    mcpServers = result.mcpServers;
     mcpServerCommand = undefined;
+
+    if (result.blockedServerNames && result.blockedServerNames.length > 0) {
+      const message = getAdminBlockedMcpServersMessage(
+        result.blockedServerNames,
+        undefined,
+      );
+      coreEvents.emitConsoleLog('warn', message);
+    }
   }
 
   return new Config({
diff --git a/packages/cli/src/config/extension-manager.ts b/packages/cli/src/config/extension-manager.ts
index 88edb500fe..820e4d4182 100644
--- a/packages/cli/src/config/extension-manager.ts
+++ b/packages/cli/src/config/extension-manager.ts
@@ -48,6 +48,8 @@ import {
   type HookEventName,
   type ResolvedExtensionSetting,
   coreEvents,
+  applyAdminAllowlist,
+  getAdminBlockedMcpServersMessage,
 } from '@google/gemini-cli-core';
 import { maybeRequestConsentOrFail } from './extensions/consent.js';
 import { resolveEnvVarsInObject } from '../utils/envVarResolver.js';
@@ -661,12 +663,33 @@ Would you like to attempt to install via "git clone" instead?`,
         if (this.settings.admin.mcp.enabled === false) {
           config.mcpServers = undefined;
         } else {
-          config.mcpServers = Object.fromEntries(
-            Object.entries(config.mcpServers).map(([key, value]) => [
-              key,
-              filterMcpConfig(value),
-            ]),
-          );
+          // Apply admin allowlist if configured
+          const adminAllowlist = this.settings.admin.mcp.config;
+          if (adminAllowlist && Object.keys(adminAllowlist).length > 0) {
+            const result = applyAdminAllowlist(
+              config.mcpServers,
+              adminAllowlist,
+            );
+            config.mcpServers = result.mcpServers;
+
+            if (result.blockedServerNames.length > 0) {
+              const message = getAdminBlockedMcpServersMessage(
+                result.blockedServerNames,
+                undefined,
+              );
+              coreEvents.emitConsoleLog('warn', message);
+            }
+          }
+
+          // Then apply local filtering/sanitization
+          if (config.mcpServers) {
+            config.mcpServers = Object.fromEntries(
+              Object.entries(config.mcpServers).map(([key, value]) => [
+                key,
+                filterMcpConfig(value),
+              ]),
+            );
+          }
         }
       }
 
diff --git a/packages/cli/src/deferred.test.ts b/packages/cli/src/deferred.test.ts
index 08cbb3a093..99b86c9827 100644
--- a/packages/cli/src/deferred.test.ts
+++ b/packages/cli/src/deferred.test.ts
@@ -167,7 +167,15 @@ describe('deferred', () => {
 
       // Now manually run it to verify it captured correctly
       await runDeferredCommand(createMockSettings().merged);
-      expect(originalHandler).toHaveBeenCalledWith(argv);
+      expect(originalHandler).toHaveBeenCalledWith(
+        expect.objectContaining({
+          settings: expect.objectContaining({
+            admin: expect.objectContaining({
+              extensions: expect.objectContaining({ enabled: true }),
+            }),
+          }),
+        }),
+      );
       expect(mockExit).toHaveBeenCalledWith(ExitCodes.SUCCESS);
     });
 
diff --git a/packages/cli/src/deferred.ts b/packages/cli/src/deferred.ts
index 309233ba45..dec6d9d114 100644
--- a/packages/cli/src/deferred.ts
+++ b/packages/cli/src/deferred.ts
@@ -63,7 +63,13 @@ export async function runDeferredCommand(settings: MergedSettings) {
     process.exit(ExitCodes.FATAL_CONFIG_ERROR);
   }
 
-  await deferredCommand.handler(deferredCommand.argv);
+  // Inject settings into argv
+  const argvWithSettings = {
+    ...deferredCommand.argv,
+    settings,
+  };
+
+  await deferredCommand.handler(argvWithSettings);
   await runExitCleanup();
   process.exit(ExitCodes.SUCCESS);
 }
diff --git a/packages/core/src/code_assist/admin/admin_controls.test.ts b/packages/core/src/code_assist/admin/admin_controls.test.ts
index 57849ae3a4..0606d7f255 100644
--- a/packages/core/src/code_assist/admin/admin_controls.test.ts
+++ b/packages/core/src/code_assist/admin/admin_controls.test.ts
@@ -20,6 +20,7 @@ import {
   sanitizeAdminSettings,
   stopAdminControlsPolling,
   getAdminErrorMessage,
+  getAdminBlockedMcpServersMessage,
 } from './admin_controls.js';
 import type { CodeAssistServer } from '../server.js';
 import type { Config } from '../../config/config.js';
@@ -759,4 +760,55 @@ describe('Admin Controls', () => {
       );
     });
   });
+
+  describe('getAdminBlockedMcpServersMessage', () => {
+    let mockConfig: Config;
+
+    beforeEach(() => {
+      mockConfig = {} as Config;
+    });
+
+    it('should show count for a single blocked server', () => {
+      vi.mocked(getCodeAssistServer).mockReturnValue({
+        projectId: 'test-project-123',
+      } as CodeAssistServer);
+
+      const message = getAdminBlockedMcpServersMessage(
+        ['server-1'],
+        mockConfig,
+      );
+
+      expect(message).toBe(
+        '1 MCP server is not allowlisted by your administrator. To enable it, please request an update to the settings at: https://goo.gle/manage-gemini-cli?project=test-project-123',
+      );
+    });
+
+    it('should show count for multiple blocked servers', () => {
+      vi.mocked(getCodeAssistServer).mockReturnValue({
+        projectId: 'test-project-123',
+      } as CodeAssistServer);
+
+      const message = getAdminBlockedMcpServersMessage(
+        ['server-1', 'server-2', 'server-3'],
+        mockConfig,
+      );
+
+      expect(message).toBe(
+        '3 MCP servers are not allowlisted by your administrator. To enable them, please request an update to the settings at: https://goo.gle/manage-gemini-cli?project=test-project-123',
+      );
+    });
+
+    it('should format message correctly with no project ID', () => {
+      vi.mocked(getCodeAssistServer).mockReturnValue(undefined);
+
+      const message = getAdminBlockedMcpServersMessage(
+        ['server-1', 'server-2'],
+        mockConfig,
+      );
+
+      expect(message).toBe(
+        '2 MCP servers are not allowlisted by your administrator. To enable them, please request an update to the settings at: https://goo.gle/manage-gemini-cli',
+      );
+    });
+  });
 });
diff --git a/packages/core/src/code_assist/admin/admin_controls.ts b/packages/core/src/code_assist/admin/admin_controls.ts
index cfd34225a6..43816215a1 100644
--- a/packages/core/src/code_assist/admin/admin_controls.ts
+++ b/packages/core/src/code_assist/admin/admin_controls.ts
@@ -238,3 +238,25 @@ export function getAdminErrorMessage(
   const projectParam = projectId ? `?project=${projectId}` : '';
   return `${featureName} is disabled by your administrator. To enable it, please request an update to the settings at: https://goo.gle/manage-gemini-cli${projectParam}`;
 }
+
+/**
+ * Returns a standardized error message for MCP servers blocked by the admin allowlist.
+ *
+ * @param blockedServers List of blocked server names
+ * @param config The application config
+ * @returns The formatted error message
+ */
+export function getAdminBlockedMcpServersMessage(
+  blockedServers: string[],
+  config: Config | undefined,
+): string {
+  const server = config ? getCodeAssistServer(config) : undefined;
+  const projectId = server?.projectId;
+  const projectParam = projectId ? `?project=${projectId}` : '';
+  const count = blockedServers.length;
+  const serverText = count === 1 ? 'server is' : 'servers are';
+
+  return `${count} MCP ${serverText} not allowlisted by your administrator. To enable ${
+    count === 1 ? 'it' : 'them'
+  }, please request an update to the settings at: https://goo.gle/manage-gemini-cli${projectParam}`;
+}
diff --git a/packages/core/src/code_assist/admin/mcpUtils.test.ts b/packages/core/src/code_assist/admin/mcpUtils.test.ts
new file mode 100644
index 0000000000..313e654d7d
--- /dev/null
+++ b/packages/core/src/code_assist/admin/mcpUtils.test.ts
@@ -0,0 +1,113 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect } from 'vitest';
+import { applyAdminAllowlist } from './mcpUtils.js';
+import type { MCPServerConfig } from '../../config/config.js';
+
+describe('applyAdminAllowlist', () => {
+  it('should return original servers if no allowlist provided', () => {
+    const localServers: Record<string, MCPServerConfig> = {
+      server1: { command: 'cmd1' },
+    };
+    expect(applyAdminAllowlist(localServers, undefined)).toEqual({
+      mcpServers: localServers,
+      blockedServerNames: [],
+    });
+  });
+
+  it('should return original servers if allowlist is empty', () => {
+    const localServers: Record<string, MCPServerConfig> = {
+      server1: { command: 'cmd1' },
+    };
+    expect(applyAdminAllowlist(localServers, {})).toEqual({
+      mcpServers: localServers,
+      blockedServerNames: [],
+    });
+  });
+
+  it('should filter servers not in allowlist', () => {
+    const localServers: Record<string, MCPServerConfig> = {
+      server1: { command: 'cmd1' },
+      server2: { command: 'cmd2' },
+    };
+    const allowlist: Record<string, MCPServerConfig> = {
+      server1: { url: 'http://server1' },
+    };
+
+    const result = applyAdminAllowlist(localServers, allowlist);
+    expect(Object.keys(result.mcpServers)).toEqual(['server1']);
+    expect(result.blockedServerNames).toEqual(['server2']);
+  });
+
+  it('should override connection details with allowlist values', () => {
+    const localServers: Record<string, MCPServerConfig> = {
+      server1: {
+        command: 'local-cmd',
+        args: ['local-arg'],
+        env: { LOCAL: 'true' },
+        description: 'Local description',
+      },
+    };
+    const allowlist: Record<string, MCPServerConfig> = {
+      server1: {
+        url: 'http://admin-url',
+        type: 'sse',
+        trust: true,
+      },
+    };
+
+    const result = applyAdminAllowlist(localServers, allowlist);
+    const server = result.mcpServers['server1'];
+
+    expect(server).toBeDefined();
+    expect(server?.url).toBe('http://admin-url');
+    expect(server?.type).toBe('sse');
+    expect(server?.trust).toBe(true);
+    // Should preserve other local fields
+    expect(server?.description).toBe('Local description');
+    // Should remove local connection fields
+    expect(server?.command).toBeUndefined();
+    expect(server?.args).toBeUndefined();
+    expect(server?.env).toBeUndefined();
+  });
+
+  it('should apply tool restrictions from allowlist', () => {
+    const localServers: Record<string, MCPServerConfig> = {
+      server1: { command: 'cmd1' },
+    };
+    const allowlist: Record<string, MCPServerConfig> = {
+      server1: {
+        url: 'http://url',
+        includeTools: ['tool1'],
+        excludeTools: ['tool2'],
+      },
+    };
+
+    const result = applyAdminAllowlist(localServers, allowlist);
+    expect(result.mcpServers['server1']?.includeTools).toEqual(['tool1']);
+    expect(result.mcpServers['server1']?.excludeTools).toEqual(['tool2']);
+  });
+
+  it('should not apply empty tool restrictions from allowlist', () => {
+    const localServers: Record<string, MCPServerConfig> = {
+      server1: {
+        command: 'cmd1',
+        includeTools: ['local-tool'],
+      },
+    };
+    const allowlist: Record<string, MCPServerConfig> = {
+      server1: {
+        url: 'http://url',
+        includeTools: [],
+      },
+    };
+
+    const result = applyAdminAllowlist(localServers, allowlist);
+    // Should keep local tool restrictions if admin ones are empty/undefined
+    expect(result.mcpServers['server1']?.includeTools).toEqual(['local-tool']);
+  });
+});
diff --git a/packages/core/src/code_assist/admin/mcpUtils.ts b/packages/core/src/code_assist/admin/mcpUtils.ts
new file mode 100644
index 0000000000..12c5845d5b
--- /dev/null
+++ b/packages/core/src/code_assist/admin/mcpUtils.ts
@@ -0,0 +1,67 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { MCPServerConfig } from '../../config/config.js';
+
+/**
+ * Applies the admin allowlist to the local MCP servers.
+ *
+ * If an admin allowlist is provided and not empty, this function filters the
+ * local servers to only those present in the allowlist. It also overrides
+ * connection details (url, type, trust) with the admin configuration and
+ * removes local execution details (command, args, env, cwd).
+ *
+ * @param localMcpServers The locally configured MCP servers.
+ * @param adminAllowlist The admin allowlist configuration.
+ * @returns The filtered and merged MCP servers.
+ */
+export function applyAdminAllowlist(
+  localMcpServers: Record<string, MCPServerConfig>,
+  adminAllowlist: Record<string, MCPServerConfig> | undefined,
+): {
+  mcpServers: Record<string, MCPServerConfig>;
+  blockedServerNames: string[];
+} {
+  if (!adminAllowlist || Object.keys(adminAllowlist).length === 0) {
+    return { mcpServers: localMcpServers, blockedServerNames: [] };
+  }
+
+  const filteredMcpServers: Record<string, MCPServerConfig> = {};
+  const blockedServerNames: string[] = [];
+
+  for (const [serverId, localConfig] of Object.entries(localMcpServers)) {
+    const adminConfig = adminAllowlist[serverId];
+    if (adminConfig) {
+      const mergedConfig = {
+        ...localConfig,
+        url: adminConfig.url,
+        type: adminConfig.type,
+        trust: adminConfig.trust,
+      };
+
+      // Remove local connection details
+      delete mergedConfig.command;
+      delete mergedConfig.args;
+      delete mergedConfig.env;
+      delete mergedConfig.cwd;
+      delete mergedConfig.httpUrl;
+      delete mergedConfig.tcp;
+
+      if (
+        (adminConfig.includeTools && adminConfig.includeTools.length > 0) ||
+        (adminConfig.excludeTools && adminConfig.excludeTools.length > 0)
+      ) {
+        mergedConfig.includeTools = adminConfig.includeTools;
+        mergedConfig.excludeTools = adminConfig.excludeTools;
+      }
+
+      filteredMcpServers[serverId] = mergedConfig;
+    } else {
+      blockedServerNames.push(serverId);
+    }
+  }
+  return { mcpServers: filteredMcpServers, blockedServerNames };
+}
diff --git a/packages/core/src/index.ts b/packages/core/src/index.ts
index b06a416176..856a896b3a 100644
--- a/packages/core/src/index.ts
+++ b/packages/core/src/index.ts
@@ -51,6 +51,7 @@ export * from './code_assist/setup.js';
 export * from './code_assist/types.js';
 export * from './code_assist/telemetry.js';
 export * from './code_assist/admin/admin_controls.js';
+export * from './code_assist/admin/mcpUtils.js';
 export * from './core/apiKeyCredentialStorage.js';
 
 // Export utilities