diff --git a/packages/cli/src/commands/extensions/enable.test.ts b/packages/cli/src/commands/extensions/enable.test.ts
index 4b08f85046..aafb5193e4 100644
--- a/packages/cli/src/commands/extensions/enable.test.ts
+++ b/packages/cli/src/commands/extensions/enable.test.ts
@@ -62,6 +62,18 @@ vi.mock('../utils.js', () => ({
   exitCli: vi.fn(),
 }));
 
+const mockEnablementInstance = vi.hoisted(() => ({
+  getDisplayState: vi.fn(),
+  enable: vi.fn(),
+  clearSessionDisable: vi.fn(),
+  autoEnableServers: vi.fn(),
+}));
+vi.mock('../../config/mcp/mcpServerEnablement.js', () => ({
+  McpServerEnablementManager: {
+    getInstance: () => mockEnablementInstance,
+  },
+}));
+
 describe('extensions enable command', () => {
   const mockLoadSettings = vi.mocked(loadSettings);
   const mockExtensionManager = vi.mocked(ExtensionManager);
@@ -75,6 +87,12 @@ describe('extensions enable command', () => {
       .fn()
       .mockResolvedValue(undefined);
     mockExtensionManager.prototype.enableExtension = vi.fn();
+    mockExtensionManager.prototype.getExtensions = vi.fn().mockReturnValue([]);
+    mockEnablementInstance.getDisplayState.mockReset();
+    mockEnablementInstance.enable.mockReset();
+    mockEnablementInstance.clearSessionDisable.mockReset();
+    mockEnablementInstance.autoEnableServers.mockReset();
+    mockEnablementInstance.autoEnableServers.mockResolvedValue([]);
   });
 
   afterEach(() => {
@@ -134,6 +152,50 @@ describe('extensions enable command', () => {
 
       mockCwd.mockRestore();
     });
+
+    it('should auto-enable disabled MCP servers for the extension', async () => {
+      const mockCwd = vi.spyOn(process, 'cwd').mockReturnValue('/test/dir');
+      mockEnablementInstance.autoEnableServers.mockResolvedValue([
+        'test-server',
+      ]);
+      mockExtensionManager.prototype.getExtensions = vi
+        .fn()
+        .mockReturnValue([
+          { name: 'my-extension', mcpServers: { 'test-server': {} } },
+        ]);
+
+      await handleEnable({ name: 'my-extension' });
+
+      expect(mockEnablementInstance.autoEnableServers).toHaveBeenCalledWith([
+        'test-server',
+      ]);
+      expect(emitConsoleLog).toHaveBeenCalledWith(
+        'log',
+        expect.stringContaining("MCP server 'test-server' was disabled"),
+      );
+      mockCwd.mockRestore();
+    });
+
+    it('should not log when MCP servers are already enabled', async () => {
+      const mockCwd = vi.spyOn(process, 'cwd').mockReturnValue('/test/dir');
+      mockEnablementInstance.autoEnableServers.mockResolvedValue([]);
+      mockExtensionManager.prototype.getExtensions = vi
+        .fn()
+        .mockReturnValue([
+          { name: 'my-extension', mcpServers: { 'test-server': {} } },
+        ]);
+
+      await handleEnable({ name: 'my-extension' });
+
+      expect(mockEnablementInstance.autoEnableServers).toHaveBeenCalledWith([
+        'test-server',
+      ]);
+      expect(emitConsoleLog).not.toHaveBeenCalledWith(
+        'log',
+        expect.stringContaining("MCP server 'test-server' was disabled"),
+      );
+      mockCwd.mockRestore();
+    });
   });
 
   describe('enableCommand', () => {
diff --git a/packages/cli/src/commands/extensions/enable.ts b/packages/cli/src/commands/extensions/enable.ts
index 67d7087d2d..55f3e596c4 100644
--- a/packages/cli/src/commands/extensions/enable.ts
+++ b/packages/cli/src/commands/extensions/enable.ts
@@ -15,6 +15,7 @@ import {
 } from '@google/gemini-cli-core';
 import { promptForSetting } from '../../config/extensions/extensionSettings.js';
 import { exitCli } from '../utils.js';
+import { McpServerEnablementManager } from '../../config/mcp/mcpServerEnablement.js';
 
 interface EnableArgs {
   name: string;
@@ -37,6 +38,26 @@ export async function handleEnable(args: EnableArgs) {
     } else {
       await extensionManager.enableExtension(args.name, SettingScope.User);
     }
+
+    // Auto-enable any disabled MCP servers for this extension
+    const extension = extensionManager
+      .getExtensions()
+      .find((e) => e.name === args.name);
+
+    if (extension?.mcpServers) {
+      const mcpEnablementManager = McpServerEnablementManager.getInstance();
+      const enabledServers = await mcpEnablementManager.autoEnableServers(
+        Object.keys(extension.mcpServers ?? {}),
+      );
+
+      for (const serverName of enabledServers) {
+        debugLogger.log(
+          `MCP server '${serverName}' was disabled - now enabled.`,
+        );
+      }
+      // Note: No restartServer() - CLI exits immediately, servers load on next session
+    }
+
     if (args.scope) {
       debugLogger.log(
         `Extension "${args.name}" successfully enabled for scope "${args.scope}".`,
diff --git a/packages/cli/src/commands/mcp/enableDisable.ts b/packages/cli/src/commands/mcp/enableDisable.ts
index f4146897eb..b47e259eca 100644
--- a/packages/cli/src/commands/mcp/enableDisable.ts
+++ b/packages/cli/src/commands/mcp/enableDisable.ts
@@ -42,21 +42,6 @@ async function handleEnable(args: Args): Promise<void> {
     return;
   }
 
-  // Check if server is from an extension
-  const serverKey = Object.keys(servers).find(
-    (key) => normalizeServerId(key) === name,
-  );
-  const server = serverKey ? servers[serverKey] : undefined;
-  if (server?.extension) {
-    debugLogger.log(
-      `${RED}Error:${RESET} Server '${args.name}' is provided by extension '${server.extension.name}'.`,
-    );
-    debugLogger.log(
-      `Use 'gemini extensions enable ${server.extension.name}' to manage this extension.`,
-    );
-    return;
-  }
-
   const result = await canLoadServer(name, {
     adminMcpEnabled: settings.merged.admin?.mcp?.enabled ?? true,
     allowedList: settings.merged.mcp?.allowed,
@@ -100,21 +85,6 @@ async function handleDisable(args: Args): Promise<void> {
     return;
   }
 
-  // Check if server is from an extension
-  const serverKey = Object.keys(servers).find(
-    (key) => normalizeServerId(key) === name,
-  );
-  const server = serverKey ? servers[serverKey] : undefined;
-  if (server?.extension) {
-    debugLogger.log(
-      `${RED}Error:${RESET} Server '${args.name}' is provided by extension '${server.extension.name}'.`,
-    );
-    debugLogger.log(
-      `Use 'gemini extensions disable ${server.extension.name}' to manage this extension.`,
-    );
-    return;
-  }
-
   if (args.session) {
     manager.disableForSession(name);
     debugLogger.log(
diff --git a/packages/cli/src/config/mcp/mcpServerEnablement.ts b/packages/cli/src/config/mcp/mcpServerEnablement.ts
index da8a7a92a8..a510dd6697 100644
--- a/packages/cli/src/config/mcp/mcpServerEnablement.ts
+++ b/packages/cli/src/config/mcp/mcpServerEnablement.ts
@@ -323,6 +323,35 @@ export class McpServerEnablementManager {
     };
   }
 
+  /**
+   * Auto-enable any disabled MCP servers by name.
+   * Returns server names that were actually re-enabled.
+   */
+  async autoEnableServers(serverNames: string[]): Promise<string[]> {
+    const enabledServers: string[] = [];
+
+    for (const serverName of serverNames) {
+      const normalizedName = normalizeServerId(serverName);
+      const state = await this.getDisplayState(normalizedName);
+
+      let wasDisabled = false;
+      if (state.isPersistentDisabled) {
+        await this.enable(normalizedName);
+        wasDisabled = true;
+      }
+      if (state.isSessionDisabled) {
+        this.clearSessionDisable(normalizedName);
+        wasDisabled = true;
+      }
+
+      if (wasDisabled) {
+        enabledServers.push(serverName);
+      }
+    }
+
+    return enabledServers;
+  }
+
   /**
    * Read config from file asynchronously.
    */
diff --git a/packages/cli/src/ui/commands/extensionsCommand.ts b/packages/cli/src/ui/commands/extensionsCommand.ts
index 6aa748153a..1258e30002 100644
--- a/packages/cli/src/ui/commands/extensionsCommand.ts
+++ b/packages/cli/src/ui/commands/extensionsCommand.ts
@@ -29,6 +29,7 @@ import {
   inferInstallMetadata,
 } from '../../config/extension-manager.js';
 import { SettingScope } from '../../config/settings.js';
+import { McpServerEnablementManager } from '../../config/mcp/mcpServerEnablement.js';
 import { theme } from '../semantic-colors.js';
 import { stat } from 'node:fs/promises';
 
@@ -381,6 +382,38 @@ async function enableAction(context: CommandContext, args: string) {
       type: MessageType.INFO,
       text: `Extension "${name}" enabled for the scope "${scope}"`,
     });
+
+    // Auto-enable any disabled MCP servers for this extension
+    const extension = extensionManager
+      .getExtensions()
+      .find((e) => e.name === name);
+
+    if (extension?.mcpServers) {
+      const mcpEnablementManager = McpServerEnablementManager.getInstance();
+      const mcpClientManager = context.services.config?.getMcpClientManager();
+      const enabledServers = await mcpEnablementManager.autoEnableServers(
+        Object.keys(extension.mcpServers ?? {}),
+      );
+
+      if (mcpClientManager && enabledServers.length > 0) {
+        const restartPromises = enabledServers.map((serverName) =>
+          mcpClientManager.restartServer(serverName).catch((error) => {
+            context.ui.addItem({
+              type: MessageType.WARNING,
+              text: `Failed to restart MCP server '${serverName}': ${getErrorMessage(error)}`,
+            });
+          }),
+        );
+        await Promise.all(restartPromises);
+      }
+
+      if (enabledServers.length > 0) {
+        context.ui.addItem({
+          type: MessageType.INFO,
+          text: `Re-enabled MCP servers: ${enabledServers.join(', ')}`,
+        });
+      }
+    }
   }
 }
 
diff --git a/packages/cli/src/ui/commands/mcpCommand.ts b/packages/cli/src/ui/commands/mcpCommand.ts
index 4f4c098918..62154eb6fd 100644
--- a/packages/cli/src/ui/commands/mcpCommand.ts
+++ b/packages/cli/src/ui/commands/mcpCommand.ts
@@ -397,19 +397,6 @@ async function handleEnableDisable(
     };
   }
 
-  // Check if server is from an extension
-  const serverKey = Object.keys(servers).find(
-    (key) => normalizeServerId(key) === name,
-  );
-  const server = serverKey ? servers[serverKey] : undefined;
-  if (server?.extension) {
-    return {
-      type: 'message',
-      messageType: 'error',
-      content: `Server '${serverName}' is provided by extension '${server.extension.name}'.\nUse '/extensions ${action} ${server.extension.name}' to manage this extension.`,
-    };
-  }
-
   const manager = McpServerEnablementManager.getInstance();
 
   if (enable) {