diff --git a/packages/core/src/config/config.test.ts b/packages/core/src/config/config.test.ts
index 886e722ba0..4a732bbedb 100644
--- a/packages/core/src/config/config.test.ts
+++ b/packages/core/src/config/config.test.ts
@@ -1036,6 +1036,44 @@ describe('Server Config (config.ts)', () => {
       expect(registeredWrappers).toHaveLength(1);
     });
 
+    it('should register subagents as tools even when they are not in allowedTools', async () => {
+      const params: ConfigParameters = {
+        ...baseParams,
+        allowedTools: ['read_file'], // codebase-investigator is NOT here
+        agents: {
+          overrides: {
+            codebase_investigator: { enabled: true },
+          },
+        },
+      };
+      const config = new Config(params);
+
+      const mockAgentDefinition = {
+        name: 'codebase-investigator',
+        description: 'Agent 1',
+        instructions: 'Inst 1',
+      };
+
+      const AgentRegistryMock = (
+        (await vi.importMock('../agents/registry.js')) as {
+          AgentRegistry: Mock;
+        }
+      ).AgentRegistry;
+      AgentRegistryMock.prototype.getAllDefinitions.mockReturnValue([
+        mockAgentDefinition,
+      ]);
+
+      const SubAgentToolMock = (
+        (await vi.importMock('../agents/subagent-tool.js')) as {
+          SubagentTool: Mock;
+        }
+      ).SubagentTool;
+
+      await config.initialize();
+
+      expect(SubAgentToolMock).toHaveBeenCalled();
+    });
+
     it('should not register subagents as tools when agents are disabled', async () => {
       const params: ConfigParameters = {
         ...baseParams,
diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index db4085c1fa..944d14fb39 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -2469,26 +2469,16 @@ export class Config {
       agentsOverrides['codebase_investigator']?.enabled !== false ||
       agentsOverrides['cli_help']?.enabled !== false
     ) {
-      const allowedTools = this.getAllowedTools();
       const definitions = this.agentRegistry.getAllDefinitions();
 
       for (const definition of definitions) {
-        const isAllowed =
-          !allowedTools || allowedTools.includes(definition.name);
-
-        if (isAllowed) {
-          try {
-            const tool = new SubagentTool(
-              definition,
-              this,
-              this.getMessageBus(),
-            );
-            registry.registerTool(tool);
-          } catch (e: unknown) {
-            debugLogger.warn(
-              `Failed to register tool for agent ${definition.name}: ${getErrorMessage(e)}`,
-            );
-          }
+        try {
+          const tool = new SubagentTool(definition, this, this.getMessageBus());
+          registry.registerTool(tool);
+        } catch (e: unknown) {
+          debugLogger.warn(
+            `Failed to register tool for agent ${definition.name}: ${getErrorMessage(e)}`,
+          );
         }
       }
     }