diff --git a/packages/a2a-server/src/config/config.test.ts b/packages/a2a-server/src/config/config.test.ts
index e68ebc4431..c676e46289 100644
--- a/packages/a2a-server/src/config/config.test.ts
+++ b/packages/a2a-server/src/config/config.test.ts
@@ -28,6 +28,7 @@ vi.mock('@google/gemini-cli-core', async (importOriginal) => {
       const mockConfig = {
         ...params,
         initialize: vi.fn(),
+        waitForMcpInit: vi.fn(),
         refreshAuth: vi.fn(),
         getExperiments: vi.fn().mockReturnValue({
           flags: {
@@ -94,6 +95,7 @@ describe('loadConfig', () => {
           const mockConfig = {
             ...(params as object),
             initialize: vi.fn(),
+            waitForMcpInit: vi.fn(),
             refreshAuth: vi.fn(),
             getExperiments: vi.fn().mockReturnValue({
               flags: {
diff --git a/packages/a2a-server/src/config/config.ts b/packages/a2a-server/src/config/config.ts
index 0873f43d98..f3100bce4d 100644
--- a/packages/a2a-server/src/config/config.ts
+++ b/packages/a2a-server/src/config/config.ts
@@ -166,6 +166,8 @@ export async function loadConfig(
 
   // Needed to initialize ToolRegistry, and git checkpointing if enabled
   await config.initialize();
+
+  await config.waitForMcpInit();
   startupProfiler.flush(config);
 
   await refreshAuthentication(config, adcFilePath, 'Config');
diff --git a/packages/cli/src/zed-integration/zedIntegration.test.ts b/packages/cli/src/zed-integration/zedIntegration.test.ts
index f3586b17f8..e8e5355dc0 100644
--- a/packages/cli/src/zed-integration/zedIntegration.test.ts
+++ b/packages/cli/src/zed-integration/zedIntegration.test.ts
@@ -129,6 +129,7 @@ describe('GeminiAgent', () => {
     mockConfig = {
       refreshAuth: vi.fn(),
       initialize: vi.fn(),
+      waitForMcpInit: vi.fn(),
       getFileSystemService: vi.fn(),
       setFileSystemService: vi.fn(),
       getContentGeneratorConfig: vi.fn(),
@@ -486,6 +487,7 @@ describe('Session', () => {
       getMessageBus: vi.fn().mockReturnValue(mockMessageBus),
       setApprovalMode: vi.fn(),
       isPlanEnabled: vi.fn().mockReturnValue(false),
+      waitForMcpInit: vi.fn(),
     } as unknown as Mocked<Config>;
     mockConnection = {
       sessionUpdate: vi.fn(),
@@ -500,6 +502,28 @@ describe('Session', () => {
     vi.clearAllMocks();
   });
 
+  it('should await MCP initialization before processing a prompt', async () => {
+    const stream = createMockStream([
+      {
+        type: StreamEventType.CHUNK,
+        value: { candidates: [{ content: { parts: [{ text: 'Hi' }] } }] },
+      },
+    ]);
+    mockChat.sendMessageStream.mockResolvedValue(stream);
+
+    await session.prompt({
+      sessionId: 'session-1',
+      prompt: [{ type: 'text', text: 'test' }],
+    });
+
+    expect(mockConfig.waitForMcpInit).toHaveBeenCalledOnce();
+    const waitOrder = (mockConfig.waitForMcpInit as Mock).mock
+      .invocationCallOrder[0];
+    const sendOrder = (mockChat.sendMessageStream as Mock).mock
+      .invocationCallOrder[0];
+    expect(waitOrder).toBeLessThan(sendOrder);
+  });
+
   it('should handle prompt with text response', async () => {
     const stream = createMockStream([
       {
diff --git a/packages/cli/src/zed-integration/zedIntegration.ts b/packages/cli/src/zed-integration/zedIntegration.ts
index 1cc9f1f3b5..98c9efdc75 100644
--- a/packages/cli/src/zed-integration/zedIntegration.ts
+++ b/packages/cli/src/zed-integration/zedIntegration.ts
@@ -521,6 +521,8 @@ export class Session {
     const pendingSend = new AbortController();
     this.pendingPrompt = pendingSend;
 
+    await this.config.waitForMcpInit();
+
     const promptId = Math.random().toString(16).slice(2);
     const chat = this.chat;
 
diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index 6262956c11..87633d35b6 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -716,6 +716,7 @@ export class Config implements McpContext {
   private compressionTruncationCounter = 0;
   private initialized = false;
   private initPromise: Promise<void> | undefined;
+  private mcpInitializationPromise: Promise<void> | null = null;
   readonly storage: Storage;
   private readonly fileExclusions: FileExclusions;
   private readonly eventEmitter?: EventEmitter;
@@ -1124,7 +1125,7 @@ export class Config implements McpContext {
     );
     // We do not await this promise so that the CLI can start up even if
     // MCP servers are slow to connect.
-    const mcpInitialization = Promise.allSettled([
+    this.mcpInitializationPromise = Promise.allSettled([
       this.mcpClientManager.startConfiguredMcpServers(),
       this.getExtensionLoader().start(this),
     ]).then((results) => {
@@ -1136,7 +1137,7 @@ export class Config implements McpContext {
     });
 
     if (!this.interactive || this.experimentalZedIntegration) {
-      await mcpInitialization;
+      await this.mcpInitializationPromise;
     }
 
     if (this.skillsSupport) {
@@ -2234,6 +2235,12 @@ export class Config implements McpContext {
     return this.experimentalZedIntegration;
   }
 
+  async waitForMcpInit(): Promise<void> {
+    if (this.mcpInitializationPromise) {
+      await this.mcpInitializationPromise;
+    }
+  }
+
   getListExtensions(): boolean {
     return this.listExtensions;
   }