diff --git a/packages/cli/src/ui/hooks/slashCommandProcessor.ts b/packages/cli/src/ui/hooks/slashCommandProcessor.ts
index c3ead63f87..238f82f9b7 100644
--- a/packages/cli/src/ui/hooks/slashCommandProcessor.ts
+++ b/packages/cli/src/ui/hooks/slashCommandProcessor.ts
@@ -28,6 +28,9 @@ import {
   ToolConfirmationOutcome,
   Storage,
   IdeClient,
+  addMCPStatusChangeListener,
+  removeMCPStatusChangeListener,
+  MCPDiscoveryState,
 } from '@google/gemini-cli-core';
 import { useSessionStats } from '../contexts/SessionContext.js';
 import type {
@@ -269,6 +272,10 @@ export const useSlashCommandProcessor = (
       ideClient.addStatusChangeListener(listener);
     })();
 
+    // Listen for MCP server status changes (e.g. connection, discovery completion)
+    // to reload slash commands (since they may include MCP prompts).
+    addMCPStatusChangeListener(listener);
+
     // TODO: Ideally this would happen more directly inside the ExtensionLoader,
     // but the CommandService today is not conducive to that since it isn't a
     // long lived service but instead gets fully re-created based on reload
@@ -289,6 +296,7 @@ export const useSlashCommandProcessor = (
         const ideClient = await IdeClient.getInstance();
         ideClient.removeStatusChangeListener(listener);
       })();
+      removeMCPStatusChangeListener(listener);
       appEvents.off('extensionsStarting', extensionEventListener);
       appEvents.off('extensionsStopping', extensionEventListener);
     };
@@ -572,9 +580,16 @@ export const useSlashCommandProcessor = (
           }
         }
 
+        const isMcpLoading =
+          config?.getMcpClientManager()?.getDiscoveryState() ===
+          MCPDiscoveryState.IN_PROGRESS;
+        const errorMessage = isMcpLoading
+          ? `Unknown command: ${trimmed}. Command might have been from an MCP server but MCP servers are not done loading.`
+          : `Unknown command: ${trimmed}`;
+
         addMessage({
           type: MessageType.ERROR,
-          content: `Unknown command: ${trimmed}`,
+          content: errorMessage,
           timestamp: new Date(),
         });
 
diff --git a/packages/cli/src/ui/hooks/useGeminiStream.test.tsx b/packages/cli/src/ui/hooks/useGeminiStream.test.tsx
index c5a004a437..d3a3ad2836 100644
--- a/packages/cli/src/ui/hooks/useGeminiStream.test.tsx
+++ b/packages/cli/src/ui/hooks/useGeminiStream.test.tsx
@@ -36,6 +36,7 @@ import {
   debugLogger,
   coreEvents,
   CoreEvent,
+  MCPDiscoveryState,
 } from '@google/gemini-cli-core';
 import type { Part, PartListUnion } from '@google/genai';
 import type { UseHistoryManagerReturn } from './useHistoryManager.js';
@@ -178,6 +179,11 @@ describe('useGeminiStream', () => {
       return clientInstance;
     });
 
+    const mockMcpClientManager = {
+      getDiscoveryState: vi.fn().mockReturnValue(MCPDiscoveryState.COMPLETED),
+      getMcpServerCount: vi.fn().mockReturnValue(0),
+    };
+
     const contentGeneratorConfig = {
       model: 'test-model',
       apiKey: 'test-key',
@@ -211,6 +217,7 @@ describe('useGeminiStream', () => {
       getProjectRoot: vi.fn(() => '/test/dir'),
       getCheckpointingEnabled: vi.fn(() => false),
       getGeminiClient: mockGetGeminiClient,
+      getMcpClientManager: () => mockMcpClientManager as any,
       getApprovalMode: () => ApprovalMode.DEFAULT,
       getUsageStatisticsEnabled: () => true,
       getDebugMode: () => false,
@@ -254,6 +261,7 @@ describe('useGeminiStream', () => {
       .mockClear()
       .mockReturnValue((async function* () {})());
     handleAtCommandSpy = vi.spyOn(atCommandProcessor, 'handleAtCommand');
+    vi.spyOn(coreEvents, 'emitFeedback');
   });
 
   const mockLoadedSettings: LoadedSettings = {
@@ -1954,6 +1962,73 @@ describe('useGeminiStream', () => {
     });
   });
 
+  describe('MCP Discovery State', () => {
+    it('should block non-slash command queries when discovery is in progress and servers exist', async () => {
+      const mockMcpClientManager = {
+        getDiscoveryState: vi
+          .fn()
+          .mockReturnValue(MCPDiscoveryState.IN_PROGRESS),
+        getMcpServerCount: vi.fn().mockReturnValue(1),
+      };
+      mockConfig.getMcpClientManager = () => mockMcpClientManager as any;
+
+      const { result } = renderTestHook();
+
+      await act(async () => {
+        await result.current.submitQuery('test query');
+      });
+
+      expect(coreEvents.emitFeedback).toHaveBeenCalledWith(
+        'info',
+        'Waiting for MCP servers to initialize... Slash commands are still available.',
+      );
+      expect(mockSendMessageStream).not.toHaveBeenCalled();
+    });
+
+    it('should NOT block queries when discovery is NOT_STARTED but there are no servers', async () => {
+      const mockMcpClientManager = {
+        getDiscoveryState: vi
+          .fn()
+          .mockReturnValue(MCPDiscoveryState.NOT_STARTED),
+        getMcpServerCount: vi.fn().mockReturnValue(0),
+      };
+      mockConfig.getMcpClientManager = () => mockMcpClientManager as any;
+
+      const { result } = renderTestHook();
+
+      await act(async () => {
+        await result.current.submitQuery('test query');
+      });
+
+      expect(coreEvents.emitFeedback).not.toHaveBeenCalledWith(
+        'info',
+        'Waiting for MCP servers to initialize... Slash commands are still available.',
+      );
+      expect(mockSendMessageStream).toHaveBeenCalled();
+    });
+
+    it('should NOT block slash commands even when discovery is in progress', async () => {
+      const mockMcpClientManager = {
+        getDiscoveryState: vi
+          .fn()
+          .mockReturnValue(MCPDiscoveryState.IN_PROGRESS),
+        getMcpServerCount: vi.fn().mockReturnValue(1),
+      };
+      mockConfig.getMcpClientManager = () => mockMcpClientManager as any;
+
+      const { result } = renderTestHook();
+
+      await act(async () => {
+        await result.current.submitQuery('/help');
+      });
+
+      expect(coreEvents.emitFeedback).not.toHaveBeenCalledWith(
+        'info',
+        'Waiting for MCP servers to initialize... Slash commands are still available.',
+      );
+    });
+  });
+
   describe('handleFinishedEvent', () => {
     it('should add info message for MAX_TOKENS finish reason', async () => {
       // Setup mock to return a stream with MAX_TOKENS finish reason
@@ -3015,4 +3090,68 @@ describe('useGeminiStream', () => {
       });
     });
   });
+
+  describe('MCP Server Initialization', () => {
+    it('should allow slash commands to run while MCP servers are initializing', async () => {
+      const mockMcpClientManager = {
+        getDiscoveryState: vi
+          .fn()
+          .mockReturnValue(MCPDiscoveryState.IN_PROGRESS),
+        getMcpServerCount: vi.fn().mockReturnValue(1),
+      };
+      mockConfig.getMcpClientManager = () => mockMcpClientManager as any;
+
+      const { result } = renderTestHook();
+
+      await act(async () => {
+        await result.current.submitQuery('/help');
+      });
+
+      // Slash command should be handled, and no Gemini call should be made.
+      expect(mockHandleSlashCommand).toHaveBeenCalledWith('/help');
+      expect(coreEvents.emitFeedback).not.toHaveBeenCalled();
+    });
+
+    it('should block normal prompts and provide feedback while MCP servers are initializing', async () => {
+      const mockMcpClientManager = {
+        getDiscoveryState: vi
+          .fn()
+          .mockReturnValue(MCPDiscoveryState.IN_PROGRESS),
+        getMcpServerCount: vi.fn().mockReturnValue(1),
+      };
+      mockConfig.getMcpClientManager = () => mockMcpClientManager as any;
+      const { result } = renderTestHook();
+
+      await act(async () => {
+        await result.current.submitQuery('a normal prompt');
+      });
+
+      // No slash command, no Gemini call, but feedback should be emitted.
+      expect(mockHandleSlashCommand).not.toHaveBeenCalled();
+      expect(mockSendMessageStream).not.toHaveBeenCalled();
+      expect(coreEvents.emitFeedback).toHaveBeenCalledWith(
+        'info',
+        'Waiting for MCP servers to initialize... Slash commands are still available.',
+      );
+    });
+
+    it('should allow normal prompts to run when MCP servers are finished initializing', async () => {
+      const mockMcpClientManager = {
+        getDiscoveryState: vi.fn().mockReturnValue(MCPDiscoveryState.COMPLETED),
+        getMcpServerCount: vi.fn().mockReturnValue(1),
+      };
+      mockConfig.getMcpClientManager = () => mockMcpClientManager as any;
+
+      const { result } = renderTestHook();
+
+      await act(async () => {
+        await result.current.submitQuery('a normal prompt');
+      });
+
+      // Prompt should be sent to Gemini.
+      expect(mockHandleSlashCommand).not.toHaveBeenCalled();
+      expect(mockSendMessageStream).toHaveBeenCalled();
+      expect(coreEvents.emitFeedback).not.toHaveBeenCalled();
+    });
+  });
 });
diff --git a/packages/cli/src/ui/hooks/useGeminiStream.ts b/packages/cli/src/ui/hooks/useGeminiStream.ts
index d9ec0217c7..2d3152bba8 100644
--- a/packages/cli/src/ui/hooks/useGeminiStream.ts
+++ b/packages/cli/src/ui/hooks/useGeminiStream.ts
@@ -30,6 +30,7 @@ import {
   ToolErrorType,
   coreEvents,
   CoreEvent,
+  MCPDiscoveryState,
 } from '@google/gemini-cli-core';
 import type {
   Config,
@@ -951,6 +952,26 @@ export const useGeminiStream = (
         { name: 'submitQuery' },
         async ({ metadata: spanMetadata }) => {
           spanMetadata.input = query;
+
+          const discoveryState = config
+            .getMcpClientManager()
+            ?.getDiscoveryState();
+          const mcpServerCount =
+            config.getMcpClientManager()?.getMcpServerCount() ?? 0;
+          if (
+            !options?.isContinuation &&
+            typeof query === 'string' &&
+            !isSlashCommand(query.trim()) &&
+            mcpServerCount > 0 &&
+            discoveryState !== MCPDiscoveryState.COMPLETED
+          ) {
+            coreEvents.emitFeedback(
+              'info',
+              'Waiting for MCP servers to initialize... Slash commands are still available.',
+            );
+            return;
+          }
+
           const queryId = `${Date.now()}-${Math.random()}`;
           activeQueryIdRef.current = queryId;
           if (
diff --git a/packages/core/src/config/config.test.ts b/packages/core/src/config/config.test.ts
index 225b687380..f9cc9bcdfc 100644
--- a/packages/core/src/config/config.test.ts
+++ b/packages/core/src/config/config.test.ts
@@ -274,6 +274,35 @@ describe('Server Config (config.ts)', () => {
       );
     });
 
+    it('should not await MCP initialization', async () => {
+      const config = new Config({
+        ...baseParams,
+        checkpointing: false,
+      });
+
+      const { McpClientManager } = await import(
+        '../tools/mcp-client-manager.js'
+      );
+      let mcpStarted = false;
+
+      (McpClientManager as unknown as Mock).mockImplementation(() => ({
+        startConfiguredMcpServers: vi.fn().mockImplementation(async () => {
+          await new Promise((resolve) => setTimeout(resolve, 50));
+          mcpStarted = true;
+        }),
+        getMcpInstructions: vi.fn(),
+      }));
+
+      await config.initialize();
+
+      // Should return immediately, before MCP finishes (50ms delay)
+      expect(mcpStarted).toBe(false);
+
+      // Wait for it to eventually finish to avoid open handles
+      await new Promise((resolve) => setTimeout(resolve, 60));
+      expect(mcpStarted).toBe(true);
+    });
+
     describe('getCompressionThreshold', () => {
       it('should return the local compression threshold if it is set', async () => {
         const config = new Config({
diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index 19c6f46fc3..20e1e20f7b 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -796,12 +796,14 @@ export class Config {
       this,
       this.eventEmitter,
     );
-    const initMcpHandle = startupProfiler.start('initialize_mcp_clients');
-    await Promise.all([
-      await this.mcpClientManager.startConfiguredMcpServers(),
-      await this.getExtensionLoader().start(this),
-    ]);
-    initMcpHandle?.end();
+    // We do not await this promise so that the CLI can start up even if
+    // MCP servers are slow to connect.
+    Promise.all([
+      this.mcpClientManager.startConfiguredMcpServers(),
+      this.getExtensionLoader().start(this),
+    ]).catch((error) => {
+      debugLogger.error('Error initializing MCP clients:', error);
+    });
 
     if (this.skillsSupport) {
       this.getSkillManager().setAdminSettings(this.adminSkillsEnabled);
diff --git a/packages/core/src/tools/mcp-client-manager.test.ts b/packages/core/src/tools/mcp-client-manager.test.ts
index d2fdc5d119..ba035d54f1 100644
--- a/packages/core/src/tools/mcp-client-manager.test.ts
+++ b/packages/core/src/tools/mcp-client-manager.test.ts
@@ -14,7 +14,7 @@ import {
   type MockedObject,
 } from 'vitest';
 import { McpClientManager } from './mcp-client-manager.js';
-import { McpClient } from './mcp-client.js';
+import { McpClient, MCPDiscoveryState } from './mcp-client.js';
 import type { ToolRegistry } from './tool-registry.js';
 import type { Config } from '../config/config.js';
 
@@ -71,6 +71,18 @@ describe('McpClientManager', () => {
     expect(mockedMcpClient.discover).toHaveBeenCalledOnce();
   });
 
+  it('should update global discovery state', async () => {
+    mockConfig.getMcpServers.mockReturnValue({
+      'test-server': {},
+    });
+    const manager = new McpClientManager(toolRegistry, mockConfig);
+    expect(manager.getDiscoveryState()).toBe(MCPDiscoveryState.NOT_STARTED);
+    const promise = manager.startConfiguredMcpServers();
+    expect(manager.getDiscoveryState()).toBe(MCPDiscoveryState.IN_PROGRESS);
+    await promise;
+    expect(manager.getDiscoveryState()).toBe(MCPDiscoveryState.COMPLETED);
+  });
+
   it('should not discover tools if folder is not trusted', async () => {
     mockConfig.getMcpServers.mockReturnValue({
       'test-server': {},
diff --git a/packages/core/src/tools/mcp-client-manager.ts b/packages/core/src/tools/mcp-client-manager.ts
index 7a1443e096..925edd17bc 100644
--- a/packages/core/src/tools/mcp-client-manager.ts
+++ b/packages/core/src/tools/mcp-client-manager.ts
@@ -362,4 +362,8 @@ export class McpClientManager {
     }
     return instructions.join('\n\n');
   }
+
+  getMcpServerCount(): number {
+    return this.clients.size;
+  }
 }