diff --git a/.changeset/tool-websearch-not-found-filter.md b/.changeset/tool-websearch-not-found-filter.md
new file mode 100644
index 00000000..7a9c1c2c
--- /dev/null
+++ b/.changeset/tool-websearch-not-found-filter.md
@@ -0,0 +1,6 @@
+---
+"@moonshot-ai/agent-core": patch
+"@moonshot-ai/kimi-code": patch
+---
+
+Filter unregistered profile tools from active set and warn when they require configuration.
diff --git a/packages/agent-core/src/agent/tool/index.ts b/packages/agent-core/src/agent/tool/index.ts
index 550cfeba..ffd3651a 100644
--- a/packages/agent-core/src/agent/tool/index.ts
+++ b/packages/agent-core/src/agent/tool/index.ts
@@ -38,6 +38,13 @@ export class ToolManager {
   protected enabledTools: Set<string> = new Set();
   /** Glob patterns (e.g. `mcp__*`, `mcp__github__*`) gating which MCP tools the profile exposes. */
   private mcpAccessPatterns: string[] = [];
+  /**
+   * Profile-requested builtin tool names that could not be resolved because
+   * `initializeBuiltinTools()` had not run yet.  Replayed once builtins are
+   * available so tools such as `WebSearch` — which require a service that may
+   * be present at init time — are not silently dropped on first profile apply.
+   */
+  private pendingBuiltinToolNames: string[] = [];
   protected readonly store: Partial<ToolStoreData> = {};
   private mcpToolStatusUnsubscribe: (() => void) | undefined;
 
@@ -297,7 +304,26 @@ export class ToolManager {
     });
     // MCP entries are glob patterns gated separately; the rest are exact
     // builtin/user tool names. The split keeps every caller on one string[].
-    this.enabledTools = new Set(names.filter((name) => !isMcpToolName(name)));
+    const nonMcpNames = names.filter((name) => !isMcpToolName(name));
+    const availableNames = nonMcpNames.filter(
+      (name) => this.builtinTools.has(name) || this.userTools.has(name),
+    );
+    const missingTools = nonMcpNames.filter((name) => !availableNames.includes(name));
+    if (missingTools.length > 0) {
+      if (this.builtinTools.size > 0) {
+        // Builtins are fully initialized — missing tools are genuinely unavailable.
+        this.agent.log.warn(
+          `The following tools listed in the active profile are not available and will be omitted: ${missingTools.join(', ')}. ` +
+            `They may require additional service configuration.`,
+        );
+      }
+      // Save pending builtin names so they can be re-applied once builtins
+      // are initialized (e.g. when the model is configured after profile apply).
+      this.pendingBuiltinToolNames = missingTools;
+    } else {
+      this.pendingBuiltinToolNames = [];
+    }
+    this.enabledTools = new Set(availableNames);
     this.mcpAccessPatterns = names.filter((name) => isMcpToolName(name));
   }
 
@@ -399,6 +425,28 @@ export class ToolManager {
         .filter((tool) => !!tool)
         .map((tool) => [tool.name, tool] as const),
     );
+    // Re-apply pending profile tool names that were deferred because builtins
+    // had not been initialized when `setActiveTools` was first called.
+    if (this.pendingBuiltinToolNames.length > 0) {
+      const nowAvailable = this.pendingBuiltinToolNames.filter(
+        (name) => this.builtinTools.has(name) || this.userTools.has(name),
+      );
+      if (nowAvailable.length > 0) {
+        for (const name of nowAvailable) {
+          this.enabledTools.add(name);
+        }
+      }
+      const stillMissing = this.pendingBuiltinToolNames.filter(
+        (name) => !nowAvailable.includes(name),
+      );
+      if (stillMissing.length > 0) {
+        this.agent.log.warn(
+          `The following tools listed in the active profile are not available and will be omitted: ${stillMissing.join(', ')}. ` +
+            `They may require additional service configuration.`,
+        );
+      }
+      this.pendingBuiltinToolNames = [];
+    }
   }
 
   private createVideoUploader(provider: ChatProvider): b.VideoUploader | undefined {
diff --git a/packages/agent-core/src/agent/turn/index.ts b/packages/agent-core/src/agent/turn/index.ts
index 068d5626..d63ec739 100644
--- a/packages/agent-core/src/agent/turn/index.ts
+++ b/packages/agent-core/src/agent/turn/index.ts
@@ -803,7 +803,7 @@ function telemetryToolOutcome(result: ToolTelemetryResult): 'success' | 'error'
 
 function telemetryToolErrorType(result: ToolTelemetryResult): string {
   const text = toolResultText(result);
-  if (text.startsWith('Tool "') && text.includes('" not found')) return 'ToolNotFound';
+  if (text.startsWith('Tool "') && (text.includes('" not found') || text.includes('is not available'))) return 'ToolNotFound';
   if (text.startsWith('Invalid args for tool "')) return 'ToolInputError';
   if (text.includes('prepareToolExecution hook failed')) return 'HookError';
   if (text.includes('finalizeToolResult hook failed')) return 'HookError';
diff --git a/packages/agent-core/src/loop/tool-call.ts b/packages/agent-core/src/loop/tool-call.ts
index c86a5705..92151138 100644
--- a/packages/agent-core/src/loop/tool-call.ts
+++ b/packages/agent-core/src/loop/tool-call.ts
@@ -167,7 +167,10 @@ function preflightToolCall(
       toolCall,
       toolName,
       args,
-      output: `Tool "${toolName}" not found`,
+      output:
+        `Tool "${toolName}" is not available. The tool was not found in the current session's tool list. ` +
+        `It may require configuration or have been removed from the active profile. ` +
+        `Use the available tools listed in your tool list instead.`,
     };
   }
   if (!parsedArgs.success) {
diff --git a/packages/agent-core/test/agent/compaction.test.ts b/packages/agent-core/test/agent/compaction.test.ts
index cbd9c437..9379e042 100644
--- a/packages/agent-core/test/agent/compaction.test.ts
+++ b/packages/agent-core/test/agent/compaction.test.ts
@@ -1499,8 +1499,8 @@ describe('Agent compaction', () => {
       [wire] context.append_loop_event   { "event": { "type": "content.part", "uuid": "<uuid-2>", "turnId": "0", "step": 1, "stepUuid": "<uuid-1>", "part": { "type": "text", "text": "I need a tool." } }, "time": "<time>" }
       [wire] context.append_loop_event   { "event": { "type": "tool.call", "uuid": "call_missing", "turnId": "0", "step": 1, "stepUuid": "<uuid-1>", "toolCallId": "call_missing", "name": "MissingTool", "args": {} }, "time": "<time>" }
       [emit] tool.call.started           { "turnId": 0, "toolCallId": "call_missing", "name": "MissingTool", "args": {} }
-      [wire] context.append_loop_event   { "event": { "type": "tool.result", "parentUuid": "call_missing", "toolCallId": "call_missing", "result": { "output": "Tool \\"MissingTool\\" not found", "isError": true } }, "time": "<time>" }
-      [emit] tool.result                 { "turnId": 0, "toolCallId": "call_missing", "output": "Tool \\"MissingTool\\" not found", "isError": true }
+      [wire] context.append_loop_event   { "event": { "type": "tool.result", "parentUuid": "call_missing", "toolCallId": "call_missing", "result": { "output": "Tool \\"MissingTool\\" is not available. The tool was not found in the current session's tool list. It may require configuration or have been removed from the active profile. Use the available tools listed in your tool list instead.", "isError": true } }, "time": "<time>" }
+      [emit] tool.result                 { "turnId": 0, "toolCallId": "call_missing", "output": "Tool \\"MissingTool\\" is not available. The tool was not found in the current session's tool list. It may require configuration or have been removed from the active profile. Use the available tools listed in your tool list instead.", "isError": true }
       [wire] context.append_loop_event   { "event": { "type": "step.end", "uuid": "<uuid-1>", "turnId": "0", "step": 1, "usage": { "inputOther": 9, "output": 11, "inputCacheRead": 0, "inputCacheCreation": 0 }, "finishReason": "tool_use" }, "time": "<time>" }
       [emit] turn.step.completed         { "turnId": 0, "step": 1, "stepId": "<uuid-1>", "usage": { "inputOther": 9, "output": 11, "inputCacheRead": 0, "inputCacheCreation": 0 }, "finishReason": "tool_use" }
       [wire] usage.record                { "model": "mock-model", "usage": { "inputOther": 9, "output": 11, "inputCacheRead": 0, "inputCacheCreation": 0 }, "usageScope": "turn", "time": "<time>" }
diff --git a/packages/agent-core/test/agent/tool.test.ts b/packages/agent-core/test/agent/tool.test.ts
index 768caf6f..f1256855 100644
--- a/packages/agent-core/test/agent/tool.test.ts
+++ b/packages/agent-core/test/agent/tool.test.ts
@@ -1,6 +1,7 @@
 import type { ToolCall } from '@moonshot-ai/kosong';
 import { describe, expect, it, vi } from 'vitest';
 
+import { ToolManager } from '../../src/agent/tool';
 import { HookEngine } from '../../src/session/hooks';
 import type { SessionSubagentHost } from '../../src/session/subagent-host';
 import { createFakeKaos } from '../tools/fixtures/fake-kaos';
@@ -9,6 +10,178 @@ import { executeTool } from '../tools/fixtures/execute-tool';
 
 const signal = new AbortController().signal;
 
+describe('ToolManager setActiveTools filtering', () => {
+  it('filters out unregistered profile tools from the active set', () => {
+    const warnings: string[] = [];
+    const agent = {
+      records: { logRecord: vi.fn() },
+      config: { hasProvider: false },
+      log: { warn: (msg: string) => { warnings.push(msg); } },
+      mcp: undefined,
+      emitEvent: vi.fn(),
+    } as unknown as import('../../src/agent').Agent;
+
+    const tm = new ToolManager(agent);
+    // Populate builtinTools map directly to simulate registered tools
+    (tm as any).builtinTools.set('Read', { name: 'Read', description: '', parameters: {}, resolveExecution: vi.fn() });
+    (tm as any).builtinTools.set('Write', { name: 'Write', description: '', parameters: {}, resolveExecution: vi.fn() });
+    (tm as any).builtinTools.set('Bash', { name: 'Bash', description: '', parameters: {}, resolveExecution: vi.fn() });
+
+    // Set active tools — WebSearch and NonExistentTool are not registered
+    tm.setActiveTools(['Read', 'Write', 'Bash', 'WebSearch', 'NonExistentTool']);
+
+    // Check active tools via toolInfos
+    const activeNames = [...tm.toolInfos()]
+      .filter((i) => i.active)
+      .map((i) => i.name)
+      .toSorted();
+    expect(activeNames).toEqual(['Bash', 'Read', 'Write']);
+
+    // Check warning was logged with missing tool names
+    expect(warnings.length).toBe(1);
+    expect(warnings[0]).toContain('are not available');
+    expect(warnings[0]).toContain('WebSearch');
+    expect(warnings[0]).toContain('NonExistentTool');
+    // Read should not be mentioned as missing
+    expect(warnings[0]).not.toContain('Read');
+  });
+
+  it('keeps all tools when all profile names are registered', () => {
+    const warnings: string[] = [];
+    const agent = {
+      records: { logRecord: vi.fn() },
+      config: { hasProvider: false },
+      log: { warn: (msg: string) => { warnings.push(msg); } },
+      mcp: undefined,
+      emitEvent: vi.fn(),
+    } as unknown as import('../../src/agent').Agent;
+
+    const tm = new ToolManager(agent);
+    (tm as any).builtinTools.set('Read', { name: 'Read', description: '', parameters: {}, resolveExecution: vi.fn() });
+    (tm as any).builtinTools.set('Write', { name: 'Write', description: '', parameters: {}, resolveExecution: vi.fn() });
+    (tm as any).builtinTools.set('Bash', { name: 'Bash', description: '', parameters: {}, resolveExecution: vi.fn() });
+    (tm as any).builtinTools.set('Grep', { name: 'Grep', description: '', parameters: {}, resolveExecution: vi.fn() });
+    (tm as any).builtinTools.set('Glob', { name: 'Glob', description: '', parameters: {}, resolveExecution: vi.fn() });
+
+    tm.setActiveTools(['Read', 'Write', 'Bash', 'Grep', 'Glob']);
+
+    const activeNames = [...tm.toolInfos()]
+      .filter((i) => i.active)
+      .map((i) => i.name)
+      .toSorted();
+    expect(activeNames).toEqual(['Bash', 'Glob', 'Grep', 'Read', 'Write']);
+    expect(warnings.length).toBe(0);
+  });
+
+  it('does not warn when all tools are available', () => {
+    const warnings: string[] = [];
+    const agent = {
+      records: { logRecord: vi.fn() },
+      config: { hasProvider: false },
+      log: { warn: (msg: string) => { warnings.push(msg); } },
+      mcp: undefined,
+      emitEvent: vi.fn(),
+    } as unknown as import('../../src/agent').Agent;
+
+    const tm = new ToolManager(agent);
+    (tm as any).builtinTools.set('Read', { name: 'Read', description: '', parameters: {}, resolveExecution: vi.fn() });
+
+    tm.setActiveTools(['Read']);
+    expect(warnings.length).toBe(0);
+  });
+
+  it('defers builtin tool names as pending when builtins not yet initialized', () => {
+    const warnings: string[] = [];
+    const agent = {
+      records: { logRecord: vi.fn() },
+      config: { hasProvider: false },
+      log: { warn: (msg: string) => { warnings.push(msg); } },
+      mcp: undefined,
+      emitEvent: vi.fn(),
+    } as unknown as import('../../src/agent').Agent;
+
+    const tm = new ToolManager(agent);
+    // builtinTools map is empty — simulate pre-initialization state
+
+    tm.setActiveTools(['Read', 'Write', 'Bash']);
+
+    // No warning because builtins are not yet initialized
+    expect(warnings.length).toBe(0);
+
+    // Active set is empty since no builtins are registered
+    const activeNames = [...tm.toolInfos()]
+      .filter((i) => i.active)
+      .map((i) => i.name);
+    expect(activeNames).toEqual([]);
+
+    // Names should be stored as pending
+    expect((tm as any).pendingBuiltinToolNames).toEqual(['Read', 'Write', 'Bash']);
+  });
+
+  it('resolves previously deferred tools when setActiveTools is recalled after builtin init', () => {
+    const makeTool = (name: string) => ({ name, description: '', parameters: {}, resolveExecution: vi.fn() });
+    const agent = {
+      records: { logRecord: vi.fn() },
+      config: { hasProvider: false },
+      log: { warn: vi.fn() },
+      mcp: undefined,
+      emitEvent: vi.fn(),
+    } as unknown as import('../../src/agent').Agent;
+
+    const tm = new ToolManager(agent);
+    // builtinTools empty — pre-init state
+
+    // First call: builtins not initialized — names deferred
+    tm.setActiveTools(['Read', 'Write']);
+    expect((tm as any).pendingBuiltinToolNames).toEqual(['Read', 'Write']);
+
+    // Builtins become available
+    (tm as any).builtinTools.set('Read', makeTool('Read'));
+    (tm as any).builtinTools.set('Write', makeTool('Write'));
+
+    // Second call: builtins populated — names resolve
+    tm.setActiveTools(['Read', 'Write']);
+    expect((tm as any).pendingBuiltinToolNames).toEqual([]);
+
+    const activeNames = [...tm.toolInfos()]
+      .filter((i) => i.active)
+      .map((i) => i.name)
+      .toSorted();
+    expect(activeNames).toEqual(['Read', 'Write']);
+    // No warning because all tools resolved
+    expect(agent.log.warn).not.toHaveBeenCalled();
+  });
+
+  it('warns about tools still missing when builtins were already initialized', () => {
+    const warnings: string[] = [];
+    const agent = {
+      records: { logRecord: vi.fn() },
+      config: { hasProvider: false },
+      log: { warn: (msg: string) => { warnings.push(msg); } },
+      mcp: undefined,
+      emitEvent: vi.fn(),
+    } as unknown as import('../../src/agent').Agent;
+
+    const tm = new ToolManager(agent);
+    // Populate builtins BEFORE setActiveTools (simulates initialized state)
+    (tm as any).builtinTools.set('Read', { name: 'Read', description: '', parameters: {}, resolveExecution: vi.fn() });
+
+    // Call setActiveTools with a genuinely missing tool
+    tm.setActiveTools(['Read', 'BogusTool']);
+
+    // Warning should fire immediately (builtins already initialized)
+    expect(warnings.length).toBe(1);
+    expect(warnings[0]).toContain('BogusTool');
+    expect(warnings[0]).toContain('not available');
+
+    // Read should be active, BogusTool should not
+    const activeNames = [...tm.toolInfos()]
+      .filter((i) => i.active)
+      .map((i) => i.name);
+    expect(activeNames).toEqual(['Read']);
+  });
+});
+
 describe('Agent tools', () => {
   it('blocks tools through PreToolUse before permission and emits PostToolUseFailure', async () => {
     const execWithEnv = vi.fn().mockRejectedValue(new Error('Bash should not execute'));