diff --git a/packages/core/src/ide/ide-client.test.ts b/packages/core/src/ide/ide-client.test.ts
index f061156d..7ad71ba3 100644
--- a/packages/core/src/ide/ide-client.test.ts
+++ b/packages/core/src/ide/ide-client.test.ts
@@ -4,75 +4,224 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { describe, it, expect } from 'vitest';
-import * as path from 'path';
-import { IdeClient } from './ide-client.js';
+import {
+  describe,
+  it,
+  expect,
+  vi,
+  beforeEach,
+  afterEach,
+  type Mocked,
+} from 'vitest';
+import { IdeClient, IDEConnectionStatus } from './ide-client.js';
+import * as fs from 'node:fs';
+import { getIdeProcessId } from './process-utils.js';
+import { Client } from '@modelcontextprotocol/sdk/client/index.js';
+import { StreamableHTTPClientTransport } from '@modelcontextprotocol/sdk/client/streamableHttp.js';
+import { StdioClientTransport } from '@modelcontextprotocol/sdk/client/stdio.js';
+import {
+  detectIde,
+  DetectedIde,
+  getIdeInfo,
+  type IdeInfo,
+} from './detect-ide.js';
+import * as os from 'node:os';
+import * as path from 'node:path';
 
-describe('IdeClient.validateWorkspacePath', () => {
-  it('should return valid if cwd is a subpath of the IDE workspace path', () => {
-    const result = IdeClient.validateWorkspacePath(
-      '/Users/person/gemini-cli',
-      'VS Code',
-      '/Users/person/gemini-cli/sub-dir',
-    );
-    expect(result.isValid).toBe(true);
+vi.mock('node:fs', async (importOriginal) => {
+  const actual = await importOriginal();
+  return {
+    ...(actual as object),
+    promises: {
+      readFile: vi.fn(),
+    },
+    realpathSync: (p: string) => p,
+    existsSync: () => false,
+  };
+});
+vi.mock('./process-utils.js');
+vi.mock('@modelcontextprotocol/sdk/client/index.js');
+vi.mock('@modelcontextprotocol/sdk/client/streamableHttp.js');
+vi.mock('@modelcontextprotocol/sdk/client/stdio.js');
+vi.mock('./detect-ide.js');
+vi.mock('node:os');
+
+describe('IdeClient', () => {
+  let mockClient: Mocked<Client>;
+  let mockHttpTransport: Mocked<StreamableHTTPClientTransport>;
+  let mockStdioTransport: Mocked<StdioClientTransport>;
+
+  beforeEach(() => {
+    // Reset singleton instance for test isolation
+    (IdeClient as unknown as { instance: IdeClient | undefined }).instance =
+      undefined;
+
+    // Mock environment variables
+    process.env['GEMINI_CLI_IDE_WORKSPACE_PATH'] = '/test/workspace';
+    delete process.env['GEMINI_CLI_IDE_SERVER_PORT'];
+    delete process.env['GEMINI_CLI_IDE_SERVER_STDIO_COMMAND'];
+    delete process.env['GEMINI_CLI_IDE_SERVER_STDIO_ARGS'];
+
+    // Mock dependencies
+    vi.spyOn(process, 'cwd').mockReturnValue('/test/workspace/sub-dir');
+    vi.mocked(detectIde).mockReturnValue(DetectedIde.VSCode);
+    vi.mocked(getIdeInfo).mockReturnValue({
+      displayName: 'VS Code',
+    } as IdeInfo);
+    vi.mocked(getIdeProcessId).mockResolvedValue(12345);
+    vi.mocked(os.tmpdir).mockReturnValue('/tmp');
+
+    // Mock MCP client and transports
+    mockClient = {
+      connect: vi.fn().mockResolvedValue(undefined),
+      close: vi.fn(),
+      setNotificationHandler: vi.fn(),
+      callTool: vi.fn(),
+    } as unknown as Mocked<Client>;
+    mockHttpTransport = {
+      close: vi.fn(),
+    } as unknown as Mocked<StreamableHTTPClientTransport>;
+    mockStdioTransport = {
+      close: vi.fn(),
+    } as unknown as Mocked<StdioClientTransport>;
+
+    vi.mocked(Client).mockReturnValue(mockClient);
+    vi.mocked(StreamableHTTPClientTransport).mockReturnValue(mockHttpTransport);
+    vi.mocked(StdioClientTransport).mockReturnValue(mockStdioTransport);
   });
 
-  it('should return invalid if GEMINI_CLI_IDE_WORKSPACE_PATH is undefined', () => {
-    const result = IdeClient.validateWorkspacePath(
-      undefined,
-      'VS Code',
-      '/Users/person/gemini-cli/sub-dir',
-    );
-    expect(result.isValid).toBe(false);
-    expect(result.error).toContain('Failed to connect');
+  afterEach(() => {
+    vi.restoreAllMocks();
   });
 
-  it('should return invalid if GEMINI_CLI_IDE_WORKSPACE_PATH is empty', () => {
-    const result = IdeClient.validateWorkspacePath(
-      '',
-      'VS Code',
-      '/Users/person/gemini-cli/sub-dir',
-    );
-    expect(result.isValid).toBe(false);
-    expect(result.error).toContain('please open a workspace folder');
-  });
+  describe('connect', () => {
+    it('should connect using HTTP when port is provided in config file', async () => {
+      const config = { port: '8080' };
+      vi.mocked(fs.promises.readFile).mockResolvedValue(JSON.stringify(config));
 
-  it('should return invalid if cwd is not within the IDE workspace path', () => {
-    const result = IdeClient.validateWorkspacePath(
-      '/some/other/path',
-      'VS Code',
-      '/Users/person/gemini-cli/sub-dir',
-    );
-    expect(result.isValid).toBe(false);
-    expect(result.error).toContain('Directory mismatch');
-  });
+      const ideClient = IdeClient.getInstance();
+      await ideClient.connect();
 
-  it('should handle multiple workspace paths and return valid', () => {
-    const result = IdeClient.validateWorkspacePath(
-      ['/some/other/path', '/Users/person/gemini-cli'].join(path.delimiter),
-      'VS Code',
-      '/Users/person/gemini-cli/sub-dir',
-    );
-    expect(result.isValid).toBe(true);
-  });
+      expect(fs.promises.readFile).toHaveBeenCalledWith(
+        path.join('/tmp', 'gemini-ide-server-12345.json'),
+        'utf8',
+      );
+      expect(StreamableHTTPClientTransport).toHaveBeenCalledWith(
+        new URL('http://localhost:8080/mcp'),
+        expect.any(Object),
+      );
+      expect(mockClient.connect).toHaveBeenCalledWith(mockHttpTransport);
+      expect(ideClient.getConnectionStatus().status).toBe(
+        IDEConnectionStatus.Connected,
+      );
+    });
 
-  it('should return invalid if cwd is not in any of the multiple workspace paths', () => {
-    const result = IdeClient.validateWorkspacePath(
-      ['/some/other/path', '/another/path'].join(path.delimiter),
-      'VS Code',
-      '/Users/person/gemini-cli/sub-dir',
-    );
-    expect(result.isValid).toBe(false);
-    expect(result.error).toContain('Directory mismatch');
-  });
+    it('should connect using stdio when stdio config is provided in file', async () => {
+      const config = { stdio: { command: 'test-cmd', args: ['--foo'] } };
+      vi.mocked(fs.promises.readFile).mockResolvedValue(JSON.stringify(config));
 
-  it.skipIf(process.platform !== 'win32')('should handle windows paths', () => {
-    const result = IdeClient.validateWorkspacePath(
-      'c:/some/other/path;d:/Users/person/gemini-cli',
-      'VS Code',
-      'd:/Users/person/gemini-cli/sub-dir',
-    );
-    expect(result.isValid).toBe(true);
+      const ideClient = IdeClient.getInstance();
+      await ideClient.connect();
+
+      expect(StdioClientTransport).toHaveBeenCalledWith({
+        command: 'test-cmd',
+        args: ['--foo'],
+      });
+      expect(mockClient.connect).toHaveBeenCalledWith(mockStdioTransport);
+      expect(ideClient.getConnectionStatus().status).toBe(
+        IDEConnectionStatus.Connected,
+      );
+    });
+
+    it('should prioritize port over stdio when both are in config file', async () => {
+      const config = {
+        port: '8080',
+        stdio: { command: 'test-cmd', args: ['--foo'] },
+      };
+      vi.mocked(fs.promises.readFile).mockResolvedValue(JSON.stringify(config));
+
+      const ideClient = IdeClient.getInstance();
+      await ideClient.connect();
+
+      expect(StreamableHTTPClientTransport).toHaveBeenCalled();
+      expect(StdioClientTransport).not.toHaveBeenCalled();
+      expect(ideClient.getConnectionStatus().status).toBe(
+        IDEConnectionStatus.Connected,
+      );
+    });
+
+    it('should connect using HTTP when port is provided in environment variables', async () => {
+      vi.mocked(fs.promises.readFile).mockRejectedValue(
+        new Error('File not found'),
+      );
+      process.env['GEMINI_CLI_IDE_SERVER_PORT'] = '9090';
+
+      const ideClient = IdeClient.getInstance();
+      await ideClient.connect();
+
+      expect(StreamableHTTPClientTransport).toHaveBeenCalledWith(
+        new URL('http://localhost:9090/mcp'),
+        expect.any(Object),
+      );
+      expect(mockClient.connect).toHaveBeenCalledWith(mockHttpTransport);
+      expect(ideClient.getConnectionStatus().status).toBe(
+        IDEConnectionStatus.Connected,
+      );
+    });
+
+    it('should connect using stdio when stdio config is in environment variables', async () => {
+      vi.mocked(fs.promises.readFile).mockRejectedValue(
+        new Error('File not found'),
+      );
+      process.env['GEMINI_CLI_IDE_SERVER_STDIO_COMMAND'] = 'env-cmd';
+      process.env['GEMINI_CLI_IDE_SERVER_STDIO_ARGS'] = '["--bar"]';
+
+      const ideClient = IdeClient.getInstance();
+      await ideClient.connect();
+
+      expect(StdioClientTransport).toHaveBeenCalledWith({
+        command: 'env-cmd',
+        args: ['--bar'],
+      });
+      expect(mockClient.connect).toHaveBeenCalledWith(mockStdioTransport);
+      expect(ideClient.getConnectionStatus().status).toBe(
+        IDEConnectionStatus.Connected,
+      );
+    });
+
+    it('should prioritize file config over environment variables', async () => {
+      const config = { port: '8080' };
+      vi.mocked(fs.promises.readFile).mockResolvedValue(JSON.stringify(config));
+      process.env['GEMINI_CLI_IDE_SERVER_PORT'] = '9090';
+
+      const ideClient = IdeClient.getInstance();
+      await ideClient.connect();
+
+      expect(StreamableHTTPClientTransport).toHaveBeenCalledWith(
+        new URL('http://localhost:8080/mcp'),
+        expect.any(Object),
+      );
+      expect(ideClient.getConnectionStatus().status).toBe(
+        IDEConnectionStatus.Connected,
+      );
+    });
+
+    it('should be disconnected if no config is found', async () => {
+      vi.mocked(fs.promises.readFile).mockRejectedValue(
+        new Error('File not found'),
+      );
+
+      const ideClient = IdeClient.getInstance();
+      await ideClient.connect();
+
+      expect(StreamableHTTPClientTransport).not.toHaveBeenCalled();
+      expect(StdioClientTransport).not.toHaveBeenCalled();
+      expect(ideClient.getConnectionStatus().status).toBe(
+        IDEConnectionStatus.Disconnected,
+      );
+      expect(ideClient.getConnectionStatus().details).toContain(
+        'Failed to connect',
+      );
+    });
   });
 });
diff --git a/packages/core/src/ide/ide-client.ts b/packages/core/src/ide/ide-client.ts
index d6b1d0d2..0f8536aa 100644
--- a/packages/core/src/ide/ide-client.ts
+++ b/packages/core/src/ide/ide-client.ts
@@ -18,6 +18,7 @@ import {
 import { getIdeProcessId } from './process-utils.js';
 import { Client } from '@modelcontextprotocol/sdk/client/index.js';
 import { StreamableHTTPClientTransport } from '@modelcontextprotocol/sdk/client/streamableHttp.js';
+import { StdioClientTransport } from '@modelcontextprotocol/sdk/client/stdio.js';
 import * as os from 'node:os';
 import * as path from 'node:path';
 import { EnvHttpProxyAgent } from 'undici';
@@ -40,6 +41,16 @@ export enum IDEConnectionStatus {
   Connecting = 'connecting',
 }
 
+type StdioConfig = {
+  command: string;
+  args: string[];
+};
+
+type ConnectionConfig = {
+  port?: string;
+  stdio?: StdioConfig;
+};
+
 function getRealPath(path: string): string {
   try {
     return fs.realpathSync(path);
@@ -104,9 +115,9 @@ export class IdeClient {
 
     this.setState(IDEConnectionStatus.Connecting);
 
-    const ideInfoFromFile = await this.getIdeInfoFromFile();
+    const configFromFile = await this.getConnectionConfigFromFile();
     const workspacePath =
-      ideInfoFromFile.workspacePath ??
+      configFromFile?.workspacePath ??
       process.env['GEMINI_CLI_IDE_WORKSPACE_PATH'];
 
     const { isValid, error } = IdeClient.validateWorkspacePath(
@@ -120,17 +131,36 @@ export class IdeClient {
       return;
     }
 
-    const portFromFile = ideInfoFromFile.port;
-    if (portFromFile) {
-      const connected = await this.establishConnection(portFromFile);
-      if (connected) {
-        return;
+    if (configFromFile) {
+      if (configFromFile.port) {
+        const connected = await this.establishHttpConnection(
+          configFromFile.port,
+        );
+        if (connected) {
+          return;
+        }
+      }
+      if (configFromFile.stdio) {
+        const connected = await this.establishStdioConnection(
+          configFromFile.stdio,
+        );
+        if (connected) {
+          return;
+        }
       }
     }
 
     const portFromEnv = this.getPortFromEnv();
     if (portFromEnv) {
-      const connected = await this.establishConnection(portFromEnv);
+      const connected = await this.establishHttpConnection(portFromEnv);
+      if (connected) {
+        return;
+      }
+    }
+
+    const stdioConfigFromEnv = this.getStdioConfigFromEnv();
+    if (stdioConfigFromEnv) {
+      const connected = await this.establishStdioConnection(stdioConfigFromEnv);
       if (connected) {
         return;
       }
@@ -316,10 +346,35 @@ export class IdeClient {
     return port;
   }
 
-  private async getIdeInfoFromFile(): Promise<{
-    port?: string;
-    workspacePath?: string;
-  }> {
+  private getStdioConfigFromEnv(): StdioConfig | undefined {
+    const command = process.env['GEMINI_CLI_IDE_SERVER_STDIO_COMMAND'];
+    if (!command) {
+      return undefined;
+    }
+
+    const argsStr = process.env['GEMINI_CLI_IDE_SERVER_STDIO_ARGS'];
+    let args: string[] = [];
+    if (argsStr) {
+      try {
+        const parsedArgs = JSON.parse(argsStr);
+        if (Array.isArray(parsedArgs)) {
+          args = parsedArgs;
+        } else {
+          logger.error(
+            'GEMINI_CLI_IDE_SERVER_STDIO_ARGS must be a JSON array string.',
+          );
+        }
+      } catch (e) {
+        logger.error('Failed to parse GEMINI_CLI_IDE_SERVER_STDIO_ARGS:', e);
+      }
+    }
+
+    return { command, args };
+  }
+
+  private async getConnectionConfigFromFile(): Promise<
+    (ConnectionConfig & { workspacePath?: string }) | undefined
+  > {
     try {
       const ideProcessId = await getIdeProcessId();
       const portFile = path.join(
@@ -327,13 +382,9 @@ export class IdeClient {
         `gemini-ide-server-${ideProcessId}.json`,
       );
       const portFileContents = await fs.promises.readFile(portFile, 'utf8');
-      const ideInfo = JSON.parse(portFileContents);
-      return {
-        port: ideInfo?.port?.toString(),
-        workspacePath: ideInfo?.workspacePath,
-      };
+      return JSON.parse(portFileContents);
     } catch (_) {
-      return {};
+      return undefined;
     }
   }
 
@@ -414,9 +465,10 @@ export class IdeClient {
     );
   }
 
-  private async establishConnection(port: string): Promise<boolean> {
+  private async establishHttpConnection(port: string): Promise<boolean> {
     let transport: StreamableHTTPClientTransport | undefined;
     try {
+      logger.debug('Attempting to connect to IDE via HTTP SSE');
       this.client = new Client({
         name: 'streamable-http-client',
         // TODO(#3487): use the CLI version here.
@@ -443,6 +495,39 @@ export class IdeClient {
       return false;
     }
   }
+
+  private async establishStdioConnection({
+    command,
+    args,
+  }: StdioConfig): Promise<boolean> {
+    let transport: StdioClientTransport | undefined;
+    try {
+      logger.debug('Attempting to connect to IDE via stdio');
+      this.client = new Client({
+        name: 'stdio-client',
+        // TODO(#3487): use the CLI version here.
+        version: '1.0.0',
+      });
+
+      transport = new StdioClientTransport({
+        command,
+        args,
+      });
+      await this.client.connect(transport);
+      this.registerClientHandlers();
+      this.setState(IDEConnectionStatus.Connected);
+      return true;
+    } catch (_error) {
+      if (transport) {
+        try {
+          await transport.close();
+        } catch (closeError) {
+          logger.debug('Failed to close transport:', closeError);
+        }
+      }
+      return false;
+    }
+  }
 }
 
 function getIdeServerHost() {