diff --git a/packages/server/src/server/agent/agent-manager.test.ts b/packages/server/src/server/agent/agent-manager.test.ts
index 41f784349e..1e8a95eb81 100644
--- a/packages/server/src/server/agent/agent-manager.test.ts
+++ b/packages/server/src/server/agent/agent-manager.test.ts
@@ -10991,6 +10991,88 @@ test("concurrent explicit closes tear down the runtime once", async () => {
   }
 });
 
+test("close drains provider tool cleanup before retiring the runtime", async () => {
+  const workdir = mkdtempSync(join(tmpdir(), "agent-manager-close-cleanup-"));
+  const storage = new AgentStorage(join(workdir, "agents"), logger);
+  const timeline = new InMemoryAgentTimelineStore();
+  class CleanupSession extends TestAgentSession {
+    override async startTurn(): Promise<{ turnId: string }> {
+      const turnId = "cleanup-turn";
+      this.pushEvent({ type: "turn_started", provider: this.provider, turnId });
+      for (const callId of ["first-tool", "second-tool"]) {
+        this.pushEvent({
+          type: "timeline",
+          provider: this.provider,
+          turnId,
+          item: {
+            type: "tool_call",
+            callId,
+            name: "Bash",
+            detail: { type: "shell", command: "sleep 10" },
+            status: "running",
+            error: null,
+          },
+        });
+      }
+      return { turnId };
+    }
+    override async close(): Promise<void> {
+      for (const callId of ["first-tool", "second-tool"]) {
+        this.pushEvent({
+          type: "timeline",
+          provider: this.provider,
+          turnId: "cleanup-turn",
+          item: {
+            type: "tool_call",
+            callId,
+            name: "Bash",
+            detail: { type: "shell", command: "sleep 10" },
+            status: "canceled",
+            error: null,
+          },
+        });
+      }
+    }
+  }
+  const client = new (class extends TestAgentClient {
+    override async createSession(config: AgentSessionConfig): Promise<AgentSession> {
+      return new CleanupSession(config);
+    }
+  })();
+  const manager = new AgentManager({
+    clients: { codex: client },
+    registry: storage,
+    timelineStore: timeline,
+    logger,
+  });
+  const agent = await manager.createAgent({ provider: "codex", cwd: workdir }, undefined, {
+    workspaceId: undefined,
+  });
+  const run = drainAsyncGenerator(manager.streamAgent(agent.id, "run both tools"));
+  try {
+    await manager.waitForAgentRunStart(agent.id);
+    await manager.flush();
+    await manager.closeAgent(agent.id);
+    await run;
+    await manager.flush();
+    expect(
+      timeline
+        .getItems(agent.id)
+        .filter((item) => item.type === "tool_call")
+        .map((item) => ({ callId: item.callId, status: item.status })),
+    ).toEqual([
+      { callId: "first-tool", status: "canceled" },
+      { callId: "second-tool", status: "canceled" },
+    ]);
+    expect((await storage.get(agent.id))?.lastStatus).toBe("closed");
+  } finally {
+    await manager.closeAgent(agent.id).catch(() => undefined);
+    await run;
+    await manager.flush();
+    rmSync(workdir, { recursive: true, force: true });
+  }
+});
+
 test("provider close failure retains the runtime for cleanup instead of allowing another writer", async () => {
   const workdir = mkdtempSync(join(tmpdir(), "agent-manager-close-failure-"));
   const storage = new AgentStorage(join(workdir, "agents"), logger);
diff --git a/packages/server/src/server/agent/agent-manager.ts b/packages/server/src/server/agent/agent-manager.ts
index 5c01be317e..dd6b7cfbb7 100644
--- a/packages/server/src/server/agent/agent-manager.ts
+++ b/packages/server/src/server/agent/agent-manager.ts
@@ -1947,6 +1947,7 @@ export class AgentManager {
     // Retain ownership until shutdown succeeds. A failed close may still own a
     // native writer, so publishing a resumable closed snapshot would orphan it.
     await agent.session.close();
+    await this.drainSessionEvents(agentId);
     this.cancelRunningProviderSubagents(agentId);
     const closedAgent = this.prepareAgentForClosure(agent, "agent closed");
 
diff --git a/packages/server/src/server/agent/providers/claude/agent.test.ts b/packages/server/src/server/agent/providers/claude/agent.test.ts
index 758fad2e8f..a5d15bdb24 100644
--- a/packages/server/src/server/agent/providers/claude/agent.test.ts
+++ b/packages/server/src/server/agent/providers/claude/agent.test.ts
@@ -729,6 +729,196 @@ describe("ClaudeAgentSession features", () => {
     return { queryFactory, queryMock, launches };
   }
 
+  function createStreamingQueryMock() {
+    const mock = createQueryMock();
+    const messages: SDKMessage[] = [];
+    let pending: ((result: IteratorResult<SDKMessage, void>) => void) | null = null;
+    let ended = false;
+    const finish = () => {
+      ended = true;
+      pending?.({ done: true, value: undefined });
+      pending = null;
+    };
+    mock.queryMock.close.mockImplementation(finish);
+    mock.queryMock.return.mockImplementation(async () => finish());
+    mock.queryMock[Symbol.asyncIterator] = () => ({
+      next: async () => {
+        const message = messages.shift();
+        if (message) return { done: false, value: message };
+        if (ended) return { done: true, value: undefined };
+        return new Promise<IteratorResult<SDKMessage, void>>((resolve) => {
+          pending = resolve;
+        });
+      },
+    });
+    return {
+      ...mock,
+      push(message: SDKMessage) {
+        if (pending) {
+          pending({ done: false, value: message });
+          pending = null;
+        } else {
+          messages.push(message);
+        }
+      },
+    };
+  }
+
+  async function startToolForClosure() {
+    const mock = createStreamingQueryMock();
+    const session = await new ClaudeAgentClient({
+      logger,
+      queryFactory: mock.queryFactory,
+      resolveBinary: async () => "/test/claude/bin",
+    }).createSession({ provider: "claude", cwd: process.cwd(), modeId: "default" });
+    const events: AgentStreamEvent[] = [];
+    let toolStarted!: () => void;
+    const running = new Promise<void>((resolve) => {
+      toolStarted = resolve;
+    });
+    const unsubscribe = session.subscribe((event) => {
+      events.push(event);
+      if (
+        event.type === "timeline" &&
+        event.item.type === "tool_call" &&
+        event.item.status === "running"
+      )
+        toolStarted();
+    });
+    await session.startTurn("run the tool");
+    mock.push({
+      type: "stream_event",
+      session_id: "closure-session",
+      uuid: "00000000-0000-4000-8000-000000000001",
+      parent_tool_use_id: null,
+      event: {
+        type: "content_block_start",
+        index: 0,
+        content_block: { type: "tool_use", id: "closure-tool", name: "Bash", input: {} },
+      },
+    });
+    mock.push({
+      type: "stream_event",
+      session_id: "closure-session",
+      uuid: "00000000-0000-4000-8000-000000000002",
+      parent_tool_use_id: null,
+      event: { type: "content_block_stop", index: 0 },
+    });
+    await running;
+    return { ...mock, session, events, unsubscribe };
+  }
+
+  test("runtime close publishes tool cleanup without reporting a user turn cancellation", async () => {
+    const fixture = await startToolForClosure();
+    try {
+      await fixture.session.close();
+      expect(fixture.queryMock.close).toHaveBeenCalledTimes(1);
+      expect(
+        fixture.events.filter(
+          (event) =>
+            event.type === "timeline" &&
+            event.item.type === "tool_call" &&
+            event.item.status === "canceled",
+        ),
+      ).toHaveLength(1);
+      expect(
+        fixture.events.filter(
+          (event) =>
+            event.type === "turn_canceled" ||
+            event.type === "turn_completed" ||
+            event.type === "turn_failed",
+        ),
+      ).toEqual([]);
+    } finally {
+      fixture.unsubscribe();
+      await fixture.session.close();
+    }
+  });
+
+  test("explicit interruption still publishes tool cleanup and one turn cancellation", async () => {
+    const fixture = await startToolForClosure();
+    try {
+      await fixture.session.interrupt();
+      expect(
+        fixture.events.filter(
+          (event) =>
+            event.type === "timeline" &&
+            event.item.type === "tool_call" &&
+            event.item.status === "canceled",
+        ),
+      ).toHaveLength(1);
+      expect(fixture.events.filter((event) => event.type === "turn_canceled")).toHaveLength(1);
+    } finally {
+      fixture.unsubscribe();
+      await fixture.session.close();
+    }
+  });
+
+  test("runtime close resolves permissions once without reporting a user turn cancellation", async () => {
+    const { queryFactory } = createQueryMock();
+    const session = await new ClaudeAgentClient({
+      logger,
+      queryFactory,
+      resolveBinary: async () => "/test/claude/bin",
+    }).createSession({ provider: "claude", cwd: process.cwd(), modeId: "default" });
+    const events: AgentStreamEvent[] = [];
+    const unsubscribe = session.subscribe((event) => events.push(event));
+    const abort = new AbortController();
+    try {
+      await session.startTurn("run the tool");
+      const canUseTool = queryFactory.mock.calls[0]?.[0].options.canUseTool;
+      if (!canUseTool) throw new Error("Expected canUseTool callback");
+      const permission = canUseTool(
+        "Bash",
+        { command: "printf test" },
+        { signal: abort.signal, toolUseID: "tool-closed" },
+      );
+      const rejected = expect(permission).rejects.toThrow("Claude session closed");
+      await session.close();
+      abort.abort();
+      await rejected;
+      expect(session.getPendingPermissions()).toEqual([]);
+      expect(events.filter(isPermissionResolvedEvent)).toHaveLength(1);
+      expect(events.filter((event) => event.type === "turn_canceled")).toEqual([]);
+    } finally {
+      unsubscribe();
+      await session.close();
+    }
+  });
+
+  test("runtime close prevents a query from launching after pending options resolve", async () => {
+    const { queryFactory } = createQueryMock();
+    let optionsStarted!: () => void;
+    let allowOptions!: () => void;
+    const started = new Promise<void>((resolve) => {
+      optionsStarted = resolve;
+    });
+    const allowed = new Promise<void>((resolve) => {
+      allowOptions = resolve;
+    });
+    const session = await new ClaudeAgentClient({
+      logger,
+      queryFactory,
+      resolveBinary: async () => {
+        optionsStarted();
+        await allowed;
+        return "/test/claude/bin";
+      },
+    }).createSession({ provider: "claude", cwd: process.cwd(), modeId: "default" });
+    const turn = session.startTurn("must not run after closure");
+    try {
+      await started;
+      await session.close();
+      allowOptions();
+      await turn;
+      expect(queryFactory).not.toHaveBeenCalled();
+    } finally {
+      allowOptions();
+      await turn;
+      await session.close();
+    }
+  });
+
   test("publishes a resolution when the SDK aborts a permission callback", async () => {
     const { queryFactory } = createQueryMock();
     const session = await new ClaudeAgentClient({
diff --git a/packages/server/src/server/agent/providers/claude/agent.ts b/packages/server/src/server/agent/providers/claude/agent.ts
index cc30825f94..9b560747fc 100644
--- a/packages/server/src/server/agent/providers/claude/agent.ts
+++ b/packages/server/src/server/agent/providers/claude/agent.ts
@@ -3018,7 +3018,9 @@ class ClaudeAgentSession implements AgentSession {
     this.closed = true;
     await this.ensureHistoryReady();
     this.rejectAllPendingPermissions(new Error("Claude session closed"));
-    this.cancelCurrentTurn?.();
+    // AgentManager settles the run after runtime release. Preserve cleanup records
+    // without reporting this closure as an explicit turn cancellation.
+    this.flushPendingToolCalls();
     this.subscribers.clear();
     this.activeForegroundTurnId = null;
     this.activeForegroundQuery = null;
@@ -3525,6 +3527,8 @@ class ClaudeAgentSession implements AgentSession {
 
     const input = createAsyncMessageInput<SDKUserMessage>();
     const options = await this.buildOptions(launchMode);
+    // Closure can finish while launch options are being prepared.
+    if (this.closed) throw new Error("Claude session is closed");
     this.logger.debug({ options: summarizeClaudeOptionsForLog(options) }, "claude query");
     this.input = input;
     this.runtimeSafety.reset();