diff --git a/packages/core/src/tools/mcp-client-manager.test.ts b/packages/core/src/tools/mcp-client-manager.test.ts
index b30425c8f4..6095381841 100644
--- a/packages/core/src/tools/mcp-client-manager.test.ts
+++ b/packages/core/src/tools/mcp-client-manager.test.ts
@@ -10,6 +10,7 @@ import { McpClient } from './mcp-client.js';
 import type { ToolRegistry } from './tool-registry.js';
 import type { PromptRegistry } from '../prompts/prompt-registry.js';
 import type { WorkspaceContext } from '../utils/workspaceContext.js';
+import type { Config } from '../config/config.js';
 
 vi.mock('./mcp-client.js', async () => {
   const originalModule = await vi.importActual('./mcp-client.js');
@@ -47,8 +48,64 @@ describe('McpClientManager', () => {
       false,
       {} as WorkspaceContext,
     );
-    await manager.discoverAllMcpTools();
+    await manager.discoverAllMcpTools({
+      isTrustedFolder: () => true,
+    } as unknown as Config);
     expect(mockedMcpClient.connect).toHaveBeenCalledOnce();
     expect(mockedMcpClient.discover).toHaveBeenCalledOnce();
   });
+
+  it('should discover tools if isTrustedFolder is undefined', async () => {
+    const mockedMcpClient = {
+      connect: vi.fn(),
+      discover: vi.fn(),
+      disconnect: vi.fn(),
+      getStatus: vi.fn(),
+    };
+    vi.mocked(McpClient).mockReturnValue(
+      mockedMcpClient as unknown as McpClient,
+    );
+    const manager = new McpClientManager(
+      {
+        'test-server': {},
+      },
+      '',
+      {} as ToolRegistry,
+      {} as PromptRegistry,
+      false,
+      {} as WorkspaceContext,
+    );
+    await manager.discoverAllMcpTools({
+      isTrustedFolder: () => undefined,
+    } as unknown as Config);
+    expect(mockedMcpClient.connect).toHaveBeenCalledOnce();
+    expect(mockedMcpClient.discover).toHaveBeenCalledOnce();
+  });
+
+  it('should not discover tools if folder is not trusted', async () => {
+    const mockedMcpClient = {
+      connect: vi.fn(),
+      discover: vi.fn(),
+      disconnect: vi.fn(),
+      getStatus: vi.fn(),
+    };
+    vi.mocked(McpClient).mockReturnValue(
+      mockedMcpClient as unknown as McpClient,
+    );
+    const manager = new McpClientManager(
+      {
+        'test-server': {},
+      },
+      '',
+      {} as ToolRegistry,
+      {} as PromptRegistry,
+      false,
+      {} as WorkspaceContext,
+    );
+    await manager.discoverAllMcpTools({
+      isTrustedFolder: () => false,
+    } as unknown as Config);
+    expect(mockedMcpClient.connect).not.toHaveBeenCalled();
+    expect(mockedMcpClient.discover).not.toHaveBeenCalled();
+  });
 });
diff --git a/packages/core/src/tools/mcp-client-manager.ts b/packages/core/src/tools/mcp-client-manager.ts
index 182977efe6..3f25102af6 100644
--- a/packages/core/src/tools/mcp-client-manager.ts
+++ b/packages/core/src/tools/mcp-client-manager.ts
@@ -4,7 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import type { MCPServerConfig } from '../config/config.js';
+import type { Config, MCPServerConfig } from '../config/config.js';
 import type { ToolRegistry } from './tool-registry.js';
 import type { PromptRegistry } from '../prompts/prompt-registry.js';
 import {
@@ -55,7 +55,10 @@ export class McpClientManager {
    * It connects to each server, discovers its available tools, and registers
    * them with the `ToolRegistry`.
    */
-  async discoverAllMcpTools(): Promise<void> {
+  async discoverAllMcpTools(cliConfig: Config): Promise<void> {
+    if (cliConfig.isTrustedFolder() === false) {
+      return;
+    }
     await this.stop();
 
     const servers = populateMcpServerCommand(
@@ -91,7 +94,7 @@ export class McpClientManager {
 
         try {
           await client.connect();
-          await client.discover();
+          await client.discover(cliConfig);
           this.eventEmitter?.emit('mcp-server-connected', {
             name,
             current,
diff --git a/packages/core/src/tools/mcp-client.test.ts b/packages/core/src/tools/mcp-client.test.ts
index d97686de2f..d2c87bb8e4 100644
--- a/packages/core/src/tools/mcp-client.test.ts
+++ b/packages/core/src/tools/mcp-client.test.ts
@@ -19,7 +19,7 @@ import * as SdkClientStdioLib from '@modelcontextprotocol/sdk/client/stdio.js';
 import * as ClientLib from '@modelcontextprotocol/sdk/client/index.js';
 import * as GenAiLib from '@google/genai';
 import { GoogleCredentialProvider } from '../mcp/google-auth-provider.js';
-import { AuthProviderType } from '../config/config.js';
+import { AuthProviderType, type Config } from '../config/config.js';
 import type { PromptRegistry } from '../prompts/prompt-registry.js';
 import type { ToolRegistry } from './tool-registry.js';
 import type { WorkspaceContext } from '../utils/workspaceContext.js';
@@ -74,7 +74,7 @@ describe('mcp-client', () => {
         false,
       );
       await client.connect();
-      await client.discover();
+      await client.discover({} as Config);
       expect(mockedMcpToTool).toHaveBeenCalledOnce();
     });
 
@@ -136,7 +136,7 @@ describe('mcp-client', () => {
         false,
       );
       await client.connect();
-      await client.discover();
+      await client.discover({} as Config);
       expect(mockedToolRegistry.registerTool).toHaveBeenCalledOnce();
       expect(consoleWarnSpy).toHaveBeenCalledOnce();
       expect(consoleWarnSpy).toHaveBeenCalledWith(
@@ -180,7 +180,7 @@ describe('mcp-client', () => {
         false,
       );
       await client.connect();
-      await expect(client.discover()).rejects.toThrow(
+      await expect(client.discover({} as Config)).rejects.toThrow(
         'No prompts or tools found on the server.',
       );
       expect(consoleErrorSpy).toHaveBeenCalledWith(
diff --git a/packages/core/src/tools/mcp-client.ts b/packages/core/src/tools/mcp-client.ts
index 67010e9269..d34c413065 100644
--- a/packages/core/src/tools/mcp-client.ts
+++ b/packages/core/src/tools/mcp-client.ts
@@ -21,7 +21,7 @@ import {
   ListRootsRequestSchema,
 } from '@modelcontextprotocol/sdk/types.js';
 import { parse } from 'shell-quote';
-import type { MCPServerConfig } from '../config/config.js';
+import type { Config, MCPServerConfig } from '../config/config.js';
 import { AuthProviderType } from '../config/config.js';
 import { GoogleCredentialProvider } from '../mcp/google-auth-provider.js';
 import { DiscoveredMCPTool } from './mcp-tool.js';
@@ -146,13 +146,13 @@ export class McpClient {
   /**
    * Discovers tools and prompts from the MCP server.
    */
-  async discover(): Promise<void> {
+  async discover(cliConfig: Config): Promise<void> {
     if (this.status !== MCPServerStatus.CONNECTED) {
       throw new Error('Client is not connected.');
     }
 
     const prompts = await this.discoverPrompts();
-    const tools = await this.discoverTools();
+    const tools = await this.discoverTools(cliConfig);
 
     if (prompts.length === 0 && tools.length === 0) {
       throw new Error('No prompts or tools found on the server.');
@@ -191,8 +191,13 @@ export class McpClient {
     return createTransport(this.serverName, this.serverConfig, this.debugMode);
   }
 
-  private async discoverTools(): Promise<DiscoveredMCPTool[]> {
-    return discoverTools(this.serverName, this.serverConfig, this.client);
+  private async discoverTools(cliConfig: Config): Promise<DiscoveredMCPTool[]> {
+    return discoverTools(
+      this.serverName,
+      this.serverConfig,
+      this.client,
+      cliConfig,
+    );
   }
 
   private async discoverPrompts(): Promise<Prompt[]> {
@@ -445,6 +450,7 @@ export async function discoverMcpTools(
   promptRegistry: PromptRegistry,
   debugMode: boolean,
   workspaceContext: WorkspaceContext,
+  cliConfig: Config,
 ): Promise<void> {
   mcpDiscoveryState = MCPDiscoveryState.IN_PROGRESS;
   try {
@@ -459,6 +465,7 @@ export async function discoverMcpTools(
           promptRegistry,
           debugMode,
           workspaceContext,
+          cliConfig,
         ),
     );
     await Promise.all(discoveryPromises);
@@ -504,6 +511,7 @@ export async function connectAndDiscover(
   promptRegistry: PromptRegistry,
   debugMode: boolean,
   workspaceContext: WorkspaceContext,
+  cliConfig: Config,
 ): Promise<void> {
   updateMCPServerStatus(mcpServerName, MCPServerStatus.CONNECTING);
 
@@ -531,6 +539,7 @@ export async function connectAndDiscover(
       mcpServerName,
       mcpServerConfig,
       mcpClient,
+      cliConfig,
     );
 
     // If we have neither prompts nor tools, it's a failed discovery
@@ -632,6 +641,7 @@ export async function discoverTools(
   mcpServerName: string,
   mcpServerConfig: MCPServerConfig,
   mcpClient: Client,
+  cliConfig: Config,
 ): Promise<DiscoveredMCPTool[]> {
   try {
     const mcpCallableTool = mcpToTool(mcpClient);
@@ -667,6 +677,8 @@ export async function discoverTools(
             funcDecl.parametersJsonSchema ?? { type: 'object', properties: {} },
             mcpServerConfig.timeout ?? MCP_DEFAULT_TIMEOUT_MSEC,
             mcpServerConfig.trust,
+            undefined,
+            cliConfig,
           ),
         );
       } catch (error) {
diff --git a/packages/core/src/tools/mcp-tool.test.ts b/packages/core/src/tools/mcp-tool.test.ts
index b9d7ddc3ac..5fc64cbaa6 100644
--- a/packages/core/src/tools/mcp-tool.test.ts
+++ b/packages/core/src/tools/mcp-tool.test.ts
@@ -747,6 +747,89 @@ describe('DiscoveredMCPTool', () => {
     });
   });
 
+  describe('shouldConfirmExecute with folder trust', () => {
+    const mockConfig = (isTrusted: boolean | undefined) => ({
+      isTrustedFolder: () => isTrusted,
+    });
+
+    it('should return false if trust is true and folder is trusted', async () => {
+      const trustedTool = new DiscoveredMCPTool(
+        mockCallableToolInstance,
+        serverName,
+        serverToolName,
+        baseDescription,
+        inputSchema,
+        undefined,
+        true, // trust = true
+        undefined,
+        mockConfig(true) as any, // isTrustedFolder = true
+      );
+      const invocation = trustedTool.build({ param: 'mock' });
+      expect(
+        await invocation.shouldConfirmExecute(new AbortController().signal),
+      ).toBe(false);
+    });
+
+    it('should return confirmation details if trust is true but folder is not trusted', async () => {
+      const trustedTool = new DiscoveredMCPTool(
+        mockCallableToolInstance,
+        serverName,
+        serverToolName,
+        baseDescription,
+        inputSchema,
+        undefined,
+        true, // trust = true
+        undefined,
+        mockConfig(false) as any, // isTrustedFolder = false
+      );
+      const invocation = trustedTool.build({ param: 'mock' });
+      const confirmation = await invocation.shouldConfirmExecute(
+        new AbortController().signal,
+      );
+      expect(confirmation).not.toBe(false);
+      expect(confirmation).toHaveProperty('type', 'mcp');
+    });
+
+    it('should return confirmation details if trust is false, even if folder is trusted', async () => {
+      const untrustedTool = new DiscoveredMCPTool(
+        mockCallableToolInstance,
+        serverName,
+        serverToolName,
+        baseDescription,
+        inputSchema,
+        undefined,
+        false, // trust = false
+        undefined,
+        mockConfig(true) as any, // isTrustedFolder = true
+      );
+      const invocation = untrustedTool.build({ param: 'mock' });
+      const confirmation = await invocation.shouldConfirmExecute(
+        new AbortController().signal,
+      );
+      expect(confirmation).not.toBe(false);
+      expect(confirmation).toHaveProperty('type', 'mcp');
+    });
+
+    it('should return false if trust is true and folder trust is undefined', async () => {
+      // The check is `isTrustedFolder() !== false`, so `undefined` should pass
+      const trustedTool = new DiscoveredMCPTool(
+        mockCallableToolInstance,
+        serverName,
+        serverToolName,
+        baseDescription,
+        inputSchema,
+        undefined,
+        true, // trust = true
+        undefined,
+        mockConfig(undefined) as any, // isTrustedFolder = undefined
+      );
+      const invocation = trustedTool.build({ param: 'mock' });
+      expect(
+        await invocation.shouldConfirmExecute(new AbortController().signal),
+      ).toBe(false);
+    });
+  });
+
   describe('DiscoveredMCPToolInvocation', () => {
     it('should return the stringified params from getDescription', () => {
       const params = { param: 'testValue', param2: 'anotherOne' };
diff --git a/packages/core/src/tools/mcp-tool.ts b/packages/core/src/tools/mcp-tool.ts
index ede885d88e..5bc48a1e7d 100644
--- a/packages/core/src/tools/mcp-tool.ts
+++ b/packages/core/src/tools/mcp-tool.ts
@@ -19,6 +19,7 @@ import {
 } from './tools.js';
 import type { CallableTool, FunctionCall, Part } from '@google/genai';
 import { ToolErrorType } from './tool-error.js';
+import type { Config } from '../config/config.js';
 
 type ToolParams = Record<string, unknown>;
 
@@ -70,6 +71,7 @@ class DiscoveredMCPToolInvocation extends BaseToolInvocation<
     readonly timeout?: number,
     readonly trust?: boolean,
     params: ToolParams = {},
+    private readonly cliConfig?: Config,
   ) {
     super(params);
   }
@@ -80,7 +82,9 @@ class DiscoveredMCPToolInvocation extends BaseToolInvocation<
     const serverAllowListKey = this.serverName;
     const toolAllowListKey = `${this.serverName}.${this.serverToolName}`;
 
-    if (this.trust) {
+    const isTrustedFolder = this.cliConfig?.isTrustedFolder() !== false;
+
+    if (this.trust && isTrustedFolder) {
       return false; // server is trusted, no confirmation needed
     }
 
@@ -183,6 +187,7 @@ export class DiscoveredMCPTool extends BaseDeclarativeTool<
     readonly timeout?: number,
     readonly trust?: boolean,
     nameOverride?: string,
+    private readonly cliConfig?: Config,
   ) {
     super(
       nameOverride ?? generateValidName(serverToolName),
@@ -205,6 +210,7 @@ export class DiscoveredMCPTool extends BaseDeclarativeTool<
       this.timeout,
       this.trust,
       `${this.serverName}__${this.serverToolName}`,
+      this.cliConfig,
     );
   }
 
@@ -219,6 +225,7 @@ export class DiscoveredMCPTool extends BaseDeclarativeTool<
       this.timeout,
       this.trust,
       params,
+      this.cliConfig,
     );
   }
 }
diff --git a/packages/core/src/tools/tool-registry.ts b/packages/core/src/tools/tool-registry.ts
index ec054d1821..c4cb46e9b2 100644
--- a/packages/core/src/tools/tool-registry.ts
+++ b/packages/core/src/tools/tool-registry.ts
@@ -236,7 +236,7 @@ export class ToolRegistry {
     await this.discoverAndRegisterToolsFromCommand();
 
     // discover tools using MCP servers, if configured
-    await this.mcpClientManager.discoverAllMcpTools();
+    await this.mcpClientManager.discoverAllMcpTools(this.config);
   }
 
   /**
@@ -251,7 +251,7 @@ export class ToolRegistry {
     this.config.getPromptRegistry().clear();
 
     // discover tools using MCP servers, if configured
-    await this.mcpClientManager.discoverAllMcpTools();
+    await this.mcpClientManager.discoverAllMcpTools(this.config);
   }
 
   /**
@@ -285,6 +285,7 @@ export class ToolRegistry {
         this.config.getPromptRegistry(),
         this.config.getDebugMode(),
         this.config.getWorkspaceContext(),
+        this.config,
       );
     }
   }