diff --git a/packages/server/src/server/agent/providers/claude/agent.live-settings.test.ts b/packages/server/src/server/agent/providers/claude/agent.live-settings.test.ts
new file mode 100644
index 0000000000..cb272ebecb
--- /dev/null
+++ b/packages/server/src/server/agent/providers/claude/agent.live-settings.test.ts
@@ -0,0 +1,157 @@
+import { expect, test } from "vitest";
+import type { Query, SDKMessage } from "@anthropic-ai/claude-agent-sdk";
+import { createTestLogger } from "../../../../test-utils/test-logger.js";
+import type { AgentStreamEvent } from "../../agent-sdk-types.js";
+import { ClaudeAgentClient } from "./agent.js";
+import type { ClaudeQueryInput } from "./query.js";
+
+function deferred<T>() {
+  let resolve!: (value: T) => void;
+  const promise = new Promise<T>((done) => {
+    resolve = done;
+  });
+  return { promise, resolve };
+}
+
+// The injected SDK adapter consumes real session input and holds a command open
+// until the test releases it. Closing the query interrupts that command.
+class ForegroundQuery {
+  readonly work = deferred<void>();
+  readonly closed = deferred<void>();
+  private stopped = false;
+  private readonly output: AsyncGenerator<SDKMessage>;
+
+  constructor(input: ClaudeQueryInput) {
+    this.output = this.events(input);
+  }
+
+  private async *events(input: ClaudeQueryInput): AsyncGenerator<SDKMessage> {
+    if (typeof input.prompt === "string") throw new Error("Expected streaming input");
+    for await (const _prompt of input.prompt) {
+      yield {
+        type: "system",
+        subtype: "init",
+        session_id: "settings-session",
+        model: "claude-haiku-5-5",
+        permissionMode: "auto",
+      } as SDKMessage;
+      yield {
+        type: "assistant",
+        message: {
+          content: [
+            { type: "tool_use", id: "tool_sleep", name: "Bash", input: { command: "sleep 20" } },
+          ],
+        },
+      } as SDKMessage;
+      await this.work.promise;
+      if (this.stopped) return;
+      yield { type: "assistant", message: { content: "DONE" } } as SDKMessage;
+      yield {
+        type: "result",
+        subtype: "success",
+        usage: { input_tokens: 1, cache_read_input_tokens: 0, output_tokens: 1 },
+        total_cost_usd: 0,
+      } as SDKMessage;
+    }
+  }
+
+  next() {
+    return this.output.next();
+  }
+  return() {
+    this.close();
+    return this.output.return();
+  }
+  close() {
+    this.stopped = true;
+    this.closed.resolve();
+    this.work.resolve();
+  }
+  async interrupt() {
+    this.close();
+  }
+  async setPermissionMode() {}
+  async setModel() {}
+  async supportedCommands() {
+    return [];
+  }
+  [Symbol.asyncIterator]() {
+    return this;
+  }
+}
+
+test.each(["mode", "model", "commands"] as const)(
+  "a pending thinking change preserves the current turn during a %s request",
+  async (control) => {
+    const queries: ForegroundQuery[] = [];
+    const efforts: ClaudeQueryInput["options"]["effort"][] = [];
+    const client = new ClaudeAgentClient({
+      logger: createTestLogger(),
+      resolveBinary: async () => "/test/claude",
+      queryFactory: (input) => {
+        const query = new ForegroundQuery(input);
+        queries.push(query);
+        efforts.push(input.options.effort);
+        return query as unknown as Query;
+      },
+    });
+    const session = await client.createSession({
+      provider: "claude",
+      cwd: process.cwd(),
+      model: "claude-haiku-5-5",
+      modeId: "auto",
+      thinkingOptionId: "low",
+    });
+    const running = deferred<void>();
+    let terminal = deferred<string>();
+    const events: AgentStreamEvent[] = [];
+    session.subscribe((event) => {
+      events.push(event);
+      if (
+        event.type === "timeline" &&
+        event.item.type === "tool_call" &&
+        event.item.status === "running"
+      )
+        running.resolve();
+      if (
+        event.type === "turn_completed" ||
+        event.type === "turn_failed" ||
+        event.type === "turn_canceled"
+      )
+        terminal.resolve(event.type);
+    });
+    try {
+      await session.startTurn("Run the foreground command");
+      await running.promise;
+      expect(await session.setThinkingOption?.("medium")).toMatchObject({
+        message: "Thinking level applies next turn",
+      });
+      if (control === "mode") await session.setMode("acceptEdits");
+      else if (control === "model") await session.setModel("claude-sonnet-5-6");
+      else await session.listCommands();
+      queries[0].work.resolve();
+      expect(
+        await Promise.race([
+          terminal.promise,
+          queries[0].closed.promise.then(() => "query closed before turn finished"),
+        ]),
+      ).toBe("turn_completed");
+      expect(
+        events.some(
+          (event) =>
+            event.type === "timeline" &&
+            event.item.type === "assistant_message" &&
+            event.item.text === "DONE",
+        ),
+      ).toBe(true);
+
+      terminal = deferred<string>();
+      await session.startTurn("Run another command with the new thinking level");
+      queries[1].work.resolve();
+      expect(await terminal.promise).toBe("turn_completed");
+      expect(efforts).toEqual(["low", "medium"]);
+    } finally {
+      await session.close();
+    }
+  },
+);
diff --git a/packages/server/src/server/agent/providers/claude/agent.ts b/packages/server/src/server/agent/providers/claude/agent.ts
index e88ae34662..7517a87029 100644
--- a/packages/server/src/server/agent/providers/claude/agent.ts
+++ b/packages/server/src/server/agent/providers/claude/agent.ts
@@ -2610,13 +2610,13 @@ class ClaudeAgentSession implements AgentSession {
     const normalized = isPermissionMode(modeId) ? modeId : "default";
     assertClaudeModeCanRun(normalized, this.harnessEnvironment);
     const previousMode = this.currentMode;
-    const launchesQuery = !this.query || this.queryRestartNeeded;
+    const previousQuery = this.query;
     const activeQuery = await this.ensureQuery(normalized);
     try {
       await activeQuery.setPermissionMode(normalized);
     } catch (error) {
       // The query was launched in the rejected mode; relaunch in the current mode next time.
-      if (launchesQuery) this.queryRestartNeeded = true;
+      if (activeQuery !== previousQuery) this.queryRestartNeeded = true;
       throw error;
     }
     if (normalized === "plan") {
@@ -3314,7 +3314,9 @@ class ClaudeAgentSession implements AgentSession {
   }
 
   private async ensureQuery(launchMode: PermissionMode = this.currentMode): Promise<Query> {
-    if (this.query && !this.queryRestartNeeded) {
+    // Controls use the running turn's query. Pending launch settings take effect
+    // after that turn finishes, when its active query handle has been cleared.
+    if (this.query && (!this.queryRestartNeeded || this.activeForegroundQuery === this.query)) {
       return this.query;
     }
 
diff --git a/packages/server/src/server/daemon-e2e/claude-settings-mid-turn.real.e2e.test.ts b/packages/server/src/server/daemon-e2e/claude-settings-mid-turn.real.e2e.test.ts
new file mode 100644
index 0000000000..5211ff2a5a
--- /dev/null
+++ b/packages/server/src/server/daemon-e2e/claude-settings-mid-turn.real.e2e.test.ts
@@ -0,0 +1,60 @@
+import { expect, test } from "vitest";
+import { mkdtemp, rm } from "node:fs/promises";
+import { existsSync } from "node:fs";
+import { tmpdir } from "node:os";
+import path from "node:path";
+import pino from "pino";
+import { ClaudeAgentClient } from "../agent/providers/claude/agent.js";
+import { createTestPaseoDaemon } from "../test-utils/paseo-daemon.js";
+import { DaemonClient } from "../test-utils/daemon-client.js";
+
+test("changing thinking then mode preserves a foreground Claude command", async () => {
+  const logger = pino({ level: "silent" });
+  const cwd = await mkdtemp(path.join(tmpdir(), "claude-settings-mid-turn-"));
+  const daemon = await createTestPaseoDaemon({
+    logger,
+    agentClients: { claude: new ClaudeAgentClient({ logger }) },
+  });
+  const client = new DaemonClient({ url: `ws://127.0.0.1:${daemon.port}/ws` });
+  try {
+    await client.connect();
+    await client.fetchAgents({ subscribe: {} });
+    const agent = await client.createAgent({
+      provider: "claude",
+      model: "claude-haiku-5-5",
+      modeId: "auto",
+      thinkingOptionId: "low",
+      cwd,
+    });
+    await client.subscribeAgentTimeline(agent.id, () => {}).ready;
+    await client.sendMessage(
+      agent.id,
+      "Run exactly these three Bash commands in the foreground, one per tool call, in order: python3 -c \"from pathlib import Path; import time; Path('started').write_text('started'); time.sleep(20); print(1)\", then the same with print(2), then print(3). Then reply DONE.",
+    );
+    // A tool-call row is emitted before Claude's permission check finishes.
+    // Wait for the command itself, so changing to acceptEdits cannot gate its start.
+    await expect.poll(() => existsSync(path.join(cwd, "started")), { timeout: 90_000 }).toBe(true);
+    const notice = await client.setAgentThinkingOption(agent.id, "medium");
+    expect(notice).toEqual({ type: "warning", message: "Thinking level applies next turn" });
+    await client.setAgentMode(agent.id, "acceptEdits");
+    await expect
+      .poll(
+        async () => {
+          const timeline = await client.fetchAgentTimeline(agent.id, { limit: 100 });
+          return timeline.entries.some(
+            ({ item }) =>
+              item.type === "tool_call" &&
+              item.detail.type === "shell" &&
+              item.detail.command.includes("print(1)") &&
+              item.status === "completed",
+          );
+        },
+        { timeout: 45_000, interval: 100 },
+      )
+      .toBe(true);
+  } finally {
+    await client.close();
+    await daemon.close();
+    await rm(cwd, { recursive: true, force: true });
+  }
+}, 180_000);