diff --git a/packages/core/src/agents/generalist-agent.test.ts b/packages/core/src/agents/generalist-agent.test.ts
index efdf705a19..84426b926b 100644
--- a/packages/core/src/agents/generalist-agent.test.ts
+++ b/packages/core/src/agents/generalist-agent.test.ts
@@ -9,12 +9,18 @@ import { GeneralistAgent } from './generalist-agent.js';
 import { makeFakeConfig } from '../test-utils/config.js';
 import type { ToolRegistry } from '../tools/tool-registry.js';
 import type { AgentRegistry } from './registry.js';
+import { DiscoveredMCPTool } from '../tools/mcp-tool.js';
 
 describe('GeneralistAgent', () => {
   it('should create a valid generalist agent definition', () => {
     const config = makeFakeConfig();
     vi.spyOn(config, 'getToolRegistry').mockReturnValue({
       getAllToolNames: () => ['tool1', 'tool2', 'agent-tool'],
+      getAllTools: () => [
+        { name: 'tool1' },
+        { name: 'tool2' },
+        { name: 'agent-tool' },
+      ],
     } as unknown as ToolRegistry);
     vi.spyOn(config, 'getAgentRegistry').mockReturnValue({
       getDirectoryContext: () => 'mock directory context',
@@ -34,4 +40,20 @@ describe('GeneralistAgent', () => {
     // Ensure it's non-interactive
     expect(agent.promptConfig.systemPrompt).toContain('non-interactive');
   });
+
+  it('should use fully qualified names for MCP tools', () => {
+    const config = makeFakeConfig();
+    const mockMcpTool = Object.create(DiscoveredMCPTool.prototype);
+    mockMcpTool.getFullyQualifiedName = () => 'server__tool';
+    mockMcpTool.name = 'tool';
+
+    vi.spyOn(config, 'getToolRegistry').mockReturnValue({
+      getAllTools: () => [{ name: 'normal-tool' }, mockMcpTool],
+    } as unknown as ToolRegistry);
+
+    const agent = GeneralistAgent(config);
+
+    expect(agent.toolConfig?.tools).toContain('normal-tool');
+    expect(agent.toolConfig?.tools).toContain('server__tool');
+  });
 });
diff --git a/packages/core/src/agents/generalist-agent.ts b/packages/core/src/agents/generalist-agent.ts
index 1b7fc961fb..db2c56f61d 100644
--- a/packages/core/src/agents/generalist-agent.ts
+++ b/packages/core/src/agents/generalist-agent.ts
@@ -8,6 +8,7 @@ import { z } from 'zod';
 import type { Config } from '../config/config.js';
 import { getCoreSystemPrompt } from '../core/prompts.js';
 import type { LocalAgentDefinition } from './types.js';
+import { DiscoveredMCPTool } from '../tools/mcp-tool.js';
 
 const GeneralistAgentSchema = z.object({
   response: z.string().describe('The final response from the agent.'),
@@ -48,7 +49,15 @@ export const GeneralistAgent = (
     model: 'inherit',
   },
   get toolConfig() {
-    const tools = config.getToolRegistry().getAllToolNames();
+    const tools = config
+      .getToolRegistry()
+      .getAllTools()
+      .map((tool) => {
+        if (tool instanceof DiscoveredMCPTool) {
+          return tool.getFullyQualifiedName();
+        }
+        return tool.name;
+      });
     return {
       tools,
     };