diff --git a/packages/cli/src/cli-surface.test.ts b/packages/cli/src/cli-surface.test.ts
index 9011c23b3..c480fe824 100644
--- a/packages/cli/src/cli-surface.test.ts
+++ b/packages/cli/src/cli-surface.test.ts
@@ -35,6 +35,19 @@ describe("canonical CLI surface", () => {
     expect(run?.helpInformation()).not.toContain("--detach");
   });
 
+  it("offers thinking configuration when running, updating, and scheduling agents", () => {
+    const cli = createCli();
+    const run = cli.commands.find((command) => command.name() === "run");
+    const agent = cli.commands.find((command) => command.name() === "agent");
+    const update = agent?.commands.find((command) => command.name() === "update");
+    const schedule = cli.commands.find((command) => command.name() === "schedule");
+    const scheduleCreate = schedule?.commands.find((command) => command.name() === "create");
+
+    expect(run?.helpInformation()).toContain("--thinking <id>");
+    expect(update?.helpInformation()).toContain("--thinking <id>");
+    expect(scheduleCreate?.helpInformation()).toContain("--thinking <id>");
+  });
+
   it("offers opening an existing agent in the desktop app", () => {
     const agent = createCli().commands.find((command) => command.name() === "agent");
     const open = agent?.commands.find((command) => command.name() === "open");
diff --git a/packages/cli/src/commands/agent/index.ts b/packages/cli/src/commands/agent/index.ts
index a0fd5d5de..85d34ef91 100644
--- a/packages/cli/src/commands/agent/index.ts
+++ b/packages/cli/src/commands/agent/index.ts
@@ -92,9 +92,10 @@ export function createAgentCommand(): Command {
   addJsonAndDaemonHostOptions(
     agent
       .command("update")
-      .description("Update an agent's metadata")
+      .description("Update an agent's settings or metadata")
       .argument("<id>", "Agent ID (or prefix)")
       .option("--name <name>", "Update the agent's display name")
+      .option("--thinking <id>", "Update the agent's thinking option ID")
       .option(
         "--label <label>",
         "Add/set label(s) on the agent (can be used multiple times or comma-separated)",
diff --git a/packages/cli/src/commands/agent/update.test.ts b/packages/cli/src/commands/agent/update.test.ts
new file mode 100644
index 000000000..1bc328796
--- /dev/null
+++ b/packages/cli/src/commands/agent/update.test.ts
@@ -0,0 +1,108 @@
+import { describe, expect, it } from "vitest";
+import type { AgentProviderNotice } from "@getpaseo/protocol/agent-types";
+import {
+  applyAgentChanges,
+  toAgentUpdateResult,
+  type AgentMetadataChanges,
+  type AgentUpdateClient,
+} from "./update.js";
+
+class RecordingAgentUpdateClient implements AgentUpdateClient {
+  readonly metadataUpdates: Array<{
+    agentId: string;
+    updates: AgentMetadataChanges;
+  }> = [];
+  readonly thinkingUpdates: Array<{ agentId: string; thinkingOptionId: string }> = [];
+  thinkingNotice: AgentProviderNotice | null = null;
+
+  constructor(private readonly supportsThinkingUpdate = true) {}
+
+  getLastServerInfoMessage() {
+    return { features: { agentThinkingUpdate: this.supportsThinkingUpdate } };
+  }
+
+  async updateAgent(agentId: string, updates: AgentMetadataChanges): Promise<void> {
+    this.metadataUpdates.push({ agentId, updates });
+  }
+
+  async setAgentThinkingOption(
+    agentId: string,
+    thinkingOptionId: string,
+  ): Promise<AgentProviderNotice | null> {
+    this.thinkingUpdates.push({ agentId, thinkingOptionId });
+    return this.thinkingNotice;
+  }
+}
+
+describe("applyAgentChanges", () => {
+  it("updates an agent's thinking without issuing an empty metadata update", async () => {
+    const client = new RecordingAgentUpdateClient();
+
+    const result = await applyAgentChanges(client, "agent-1", {
+      type: "thinking",
+      thinkingOptionId: "high",
+    });
+
+    expect(client.metadataUpdates).toEqual([]);
+    expect(client.thinkingUpdates).toEqual([{ agentId: "agent-1", thinkingOptionId: "high" }]);
+    expect(result).toEqual({
+      notice: null,
+    });
+  });
+
+  it("requires a daemon that advertises thinking updates", async () => {
+    const client = new RecordingAgentUpdateClient(false);
+
+    await expect(
+      applyAgentChanges(client, "agent-1", { type: "thinking", thinkingOptionId: "high" }),
+    ).rejects.toMatchObject({
+      code: "DAEMON_UPDATE_REQUIRED",
+      message: "Update the host to use agent thinking updates.",
+    });
+    expect(client.metadataUpdates).toEqual([]);
+    expect(client.thinkingUpdates).toEqual([]);
+  });
+
+  it("returns the provider notice from a thinking update", async () => {
+    const client = new RecordingAgentUpdateClient();
+    client.thinkingNotice = {
+      type: "warning",
+      message: "Thinking changes apply to the next turn.",
+    };
+
+    const notice = await applyAgentChanges(client, "agent-1", {
+      type: "thinking",
+      thinkingOptionId: "high",
+    });
+
+    expect(notice).toEqual({
+      notice: {
+        type: "warning",
+        message: "Thinking changes apply to the next turn.",
+      },
+    });
+  });
+});
+
+describe("toAgentUpdateResult", () => {
+  it("reports the current thinking option after a metadata update", () => {
+    const result = toAgentUpdateResult(
+      {
+        id: "agent-1",
+        title: "Renamed agent",
+        labels: { team: "platform" },
+        effectiveThinkingOptionId: "high",
+      },
+      { notice: null },
+    );
+
+    expect(result).toEqual({
+      agentId: "agent-1",
+      name: "Renamed agent",
+      labels: "team=platform",
+      thinkingOptionId: "high",
+      noticeType: null,
+      notice: null,
+    });
+  });
+});
diff --git a/packages/cli/src/commands/agent/update.ts b/packages/cli/src/commands/agent/update.ts
index ee868afff..d23ad2d3a 100644
--- a/packages/cli/src/commands/agent/update.ts
+++ b/packages/cli/src/commands/agent/update.ts
@@ -1,4 +1,6 @@
 import type { Command } from "commander";
+import type { AgentProviderNotice } from "@getpaseo/protocol/agent-types";
+import type { AgentSnapshotPayload } from "@getpaseo/protocol/messages";
 import { connectToDaemon, getDaemonHost } from "../../utils/client.js";
 import type {
   CommandOptions,
@@ -12,6 +14,9 @@ export interface AgentUpdateResult {
   agentId: string;
   name: string | null;
   labels: string;
+  thinkingOptionId: string | null;
+  noticeType: AgentProviderNotice["type"] | null;
+  notice: string | null;
 }
 
 /** Schema for update command output */
@@ -21,17 +26,80 @@ export const updateSchema: OutputSchema<AgentUpdateResult> = {
     { header: "AGENT ID", field: "agentId" },
     { header: "NAME", field: "name" },
     { header: "LABELS", field: "labels" },
+    { header: "THINKING", field: "thinkingOptionId" },
+    { header: "NOTICE", field: "notice" },
   ],
 };
 
 export interface AgentUpdateOptions extends CommandOptions {
   name?: string;
   label?: string[];
+  thinking?: string;
   host?: string;
 }
 
 export type AgentUpdateCommandResult = SingleResult<AgentUpdateResult>;
 
+export interface AgentMetadataChanges {
+  name?: string;
+  labels?: Record<string, string>;
+}
+
+interface AgentUpdateServerInfo {
+  features?: { agentThinkingUpdate?: boolean };
+}
+
+export interface AgentUpdateClient {
+  getLastServerInfoMessage(): AgentUpdateServerInfo | null;
+  updateAgent(agentId: string, updates: AgentMetadataChanges): Promise<void>;
+  setAgentThinkingOption(
+    agentId: string,
+    thinkingOptionId: string,
+  ): Promise<AgentProviderNotice | null>;
+}
+
+export type AgentChanges =
+  | { type: "metadata"; updates: AgentMetadataChanges }
+  | { type: "thinking"; thinkingOptionId: string };
+
+export interface AppliedAgentChanges {
+  notice: AgentProviderNotice | null;
+}
+
+export function toAgentUpdateResult(
+  agent: Pick<AgentSnapshotPayload, "id" | "title" | "labels" | "effectiveThinkingOptionId">,
+  appliedChanges: AppliedAgentChanges,
+): AgentUpdateResult {
+  return {
+    agentId: agent.id,
+    name: agent.title,
+    labels: formatLabels(agent.labels),
+    thinkingOptionId: agent.effectiveThinkingOptionId ?? null,
+    noticeType: appliedChanges.notice?.type ?? null,
+    notice: appliedChanges.notice?.message ?? null,
+  };
+}
+
+export async function applyAgentChanges(
+  client: AgentUpdateClient,
+  agentId: string,
+  changes: AgentChanges,
+): Promise<AppliedAgentChanges> {
+  if (changes.type === "thinking") {
+    // COMPAT(agentThinkingUpdate): added in v0.2.4, remove gate after 2027-01-28.
+    if (client.getLastServerInfoMessage()?.features?.agentThinkingUpdate !== true) {
+      throw {
+        code: "DAEMON_UPDATE_REQUIRED",
+        message: "Update the host to use agent thinking updates.",
+      } satisfies CommandError;
+    }
+    const notice = await client.setAgentThinkingOption(agentId, changes.thinkingOptionId);
+    return { notice };
+  }
+  await client.updateAgent(agentId, changes.updates);
+  return { notice: null };
+}
+
 function parseLabelOptions(labels: string[] | undefined): Record<string, string> {
   const parsed: Record<string, string> = {};
   if (!labels) {
@@ -81,6 +149,55 @@ function formatLabels(labels: Record<string, string>): string {
   return entries.map(([key, value]) => `${key}=${value}`).join(",");
 }
 
+function parseAgentChanges(options: AgentUpdateOptions): AgentChanges {
+  const name = options.name?.trim();
+  if (options.name !== undefined && !name) {
+    throw {
+      code: "INVALID_NAME",
+      message: "Name cannot be empty",
+      details: "Use --name <name> with a non-empty value",
+    } satisfies CommandError;
+  }
+
+  const labels = parseLabelOptions(options.label);
+  const thinkingOptionId = options.thinking?.trim();
+  if (options.thinking !== undefined && !thinkingOptionId) {
+    throw {
+      code: "INVALID_THINKING_OPTION",
+      message: "--thinking cannot be empty",
+      details:
+        'Provide a thinking option ID. Use "paseo provider models <provider> --thinking" to list valid IDs.',
+    } satisfies CommandError;
+  }
+
+  const hasMetadataUpdates = Boolean(name) || Object.keys(labels).length > 0;
+  if (hasMetadataUpdates && thinkingOptionId) {
+    throw {
+      code: "INVALID_OPTIONS",
+      message: "--thinking cannot be combined with --name or --label",
+      details: "Run separate agent update commands for runtime settings and metadata.",
+    } satisfies CommandError;
+  }
+  if (!hasMetadataUpdates && !thinkingOptionId) {
+    throw {
+      code: "NO_CHANGES_PROVIDED",
+      message: "Nothing to update",
+      details: "Provide at least one of: --name <name>, --label <key=value>, --thinking <id>",
+    } satisfies CommandError;
+  }
+
+  if (thinkingOptionId) {
+    return { type: "thinking", thinkingOptionId };
+  }
+  return {
+    type: "metadata",
+    updates: {
+      ...(name ? { name } : {}),
+      ...(Object.keys(labels).length > 0 ? { labels } : {}),
+    },
+  };
+}
+
 export async function runUpdateCommand(
   agentIdArg: string,
   options: AgentUpdateOptions,
@@ -98,25 +215,7 @@ export async function runUpdateCommand(
     throw error;
   }
 
-  const name = options.name?.trim();
-  if (options.name !== undefined && !name) {
-    const error: CommandError = {
-      code: "INVALID_NAME",
-      message: "Name cannot be empty",
-      details: "Use --name <name> with a non-empty value",
-    };
-    throw error;
-  }
-
-  const labels = parseLabelOptions(options.label);
-  if (!name && Object.keys(labels).length === 0) {
-    const error: CommandError = {
-      code: "NO_CHANGES_PROVIDED",
-      message: "Nothing to update",
-      details: "Provide at least one of: --name <name>, --label <key=value>",
-    };
-    throw error;
-  }
+  const changes = parseAgentChanges(options);
 
   let client;
   try {
@@ -143,10 +242,7 @@ export async function runUpdateCommand(
     }
     const agentId = fetchResult.agent.id;
 
-    await client.updateAgent(agentId, {
-      ...(name ? { name } : {}),
-      ...(Object.keys(labels).length > 0 ? { labels } : {}),
-    });
+    const appliedChanges = await applyAgentChanges(client, agentId, changes);
 
     const updatedResult = await client.fetchAgent({ agentId });
     if (!updatedResult) {
@@ -157,11 +253,7 @@ export async function runUpdateCommand(
 
     return {
       type: "single",
-      data: {
-        agentId,
-        name: updatedResult.agent.title,
-        labels: formatLabels(updatedResult.agent.labels),
-      },
+      data: toAgentUpdateResult(updatedResult.agent, appliedChanges),
       schema: updateSchema,
     };
   } catch (err) {
diff --git a/packages/cli/src/commands/schedule/create.ts b/packages/cli/src/commands/schedule/create.ts
index 378e44675..471765876 100644
--- a/packages/cli/src/commands/schedule/create.ts
+++ b/packages/cli/src/commands/schedule/create.ts
@@ -18,6 +18,7 @@ export interface ScheduleCreateOptions extends ScheduleCommandOptions {
   target?: string;
   provider?: string;
   mode?: string;
+  thinking?: string;
   cwd?: string;
   maxRuns?: string;
   expiresIn?: string;
@@ -40,6 +41,7 @@ export async function runCreateCommand(
     target: options.target,
     provider: options.provider,
     mode: options.mode,
+    thinking: options.thinking,
     cwd: options.cwd,
     host: options.host,
     maxRuns: options.maxRuns,
diff --git a/packages/cli/src/commands/schedule/index.ts b/packages/cli/src/commands/schedule/index.ts
index f72a59b19..b006b97dd 100644
--- a/packages/cli/src/commands/schedule/index.ts
+++ b/packages/cli/src/commands/schedule/index.ts
@@ -32,6 +32,7 @@ export function createScheduleCommand(): Command {
         "--mode <mode>",
         "Provider-specific mode (e.g. claude bypassPermissions, opencode build)",
       )
+      .option("--thinking <id>", "Thinking option ID for new-agent runs")
       .option("--cwd <path>", "Working directory (default: current; required with --host)")
       .option("--run-now", "Fire one immediate run on creation")
       .option("--max-runs <n>", "Maximum number of runs")
diff --git a/packages/cli/src/commands/schedule/shared.test.ts b/packages/cli/src/commands/schedule/shared.test.ts
index d1684e7ac..25f1bb053 100644
--- a/packages/cli/src/commands/schedule/shared.test.ts
+++ b/packages/cli/src/commands/schedule/shared.test.ts
@@ -116,6 +116,25 @@ describe("parseScheduleCreateInput first-run timing", () => {
   });
 });
 
+describe("parseScheduleCreateInput thinking", () => {
+  test("sets the thinking option for each scheduled new-agent run", () => {
+    const input = parseScheduleCreateInput({
+      ...baseOptions,
+      cwd: "/project",
+      thinking: "  high  ",
+    });
+
+    expect(input.target).toEqual({
+      type: "new-agent",
+      config: {
+        provider: "claude",
+        cwd: "/project",
+        thinkingOptionId: "high",
+      },
+    });
+  });
+});
+
 describe("parseScheduleUpdateInput", () => {
   test("rejects calls with no fields to update", () => {
     expect(() => parseScheduleUpdateInput({ id: "abc" })).toThrow(
diff --git a/packages/cli/src/commands/schedule/shared.ts b/packages/cli/src/commands/schedule/shared.ts
index f70677db4..f0937dd40 100644
--- a/packages/cli/src/commands/schedule/shared.ts
+++ b/packages/cli/src/commands/schedule/shared.ts
@@ -114,7 +114,7 @@ function resolveScheduleTarget(args: {
   if (hasExplicitNewAgentOption) {
     throw {
       code: "INVALID_TARGET",
-      message: "--provider/--mode can only be used with a new-agent target",
+      message: "--provider/--mode/--thinking can only be used with a new-agent target",
       details: "Use --target new-agent or omit --target to create a new agent schedule",
     } satisfies CommandError;
   }
@@ -144,6 +144,7 @@ export function parseScheduleCreateInput(options: {
   target?: string;
   provider?: string;
   mode?: string;
+  thinking?: string;
   cwd?: string;
   host?: string;
   maxRuns?: string;
@@ -179,7 +180,15 @@ export function parseScheduleCreateInput(options: {
 
   const targetValue = options.target?.trim();
   const modeId = options.mode?.trim();
-  const hasExplicitNewAgentOption = options.provider !== undefined || options.mode !== undefined;
+  const thinkingOptionId = options.thinking?.trim();
+  if (options.thinking !== undefined && !thinkingOptionId) {
+    throw {
+      code: "INVALID_THINKING_OPTION",
+      message: "--thinking cannot be empty",
+    } satisfies CommandError;
+  }
+  const hasExplicitNewAgentOption =
+    options.provider !== undefined || options.mode !== undefined || options.thinking !== undefined;
   const createNewAgentTarget = (): ScheduleTarget => {
     const resolvedProviderModel = resolveProviderAndModel({
       provider: options.provider,
@@ -191,6 +200,7 @@ export function parseScheduleCreateInput(options: {
         cwd: cwdInput ?? process.cwd(),
         ...(resolvedProviderModel.model ? { model: resolvedProviderModel.model } : {}),
         ...(modeId ? { modeId } : {}),
+        ...(thinkingOptionId ? { thinkingOptionId } : {}),
       },
     };
   };
diff --git a/packages/cli/tests/16-agent-update.test.ts b/packages/cli/tests/16-agent-update.test.ts
index f81a6b08c..8e84ebf7b 100644
--- a/packages/cli/tests/16-agent-update.test.ts
+++ b/packages/cli/tests/16-agent-update.test.ts
@@ -33,6 +33,7 @@ try {
     assert.strictEqual(result.exitCode, 0, "agent update --help should exit 0");
     assert(result.stdout.includes("--name"), "help should mention --name flag");
     assert(result.stdout.includes("--label"), "help should mention --label flag");
+    assert(result.stdout.includes("--thinking"), "help should mention --thinking flag");
     assert(result.stdout.includes("--host"), "help should mention --host option");
     assert(result.stdout.includes("<id>"), "help should mention required id argument");
     console.log("✓ agent update --help shows options\n");
@@ -103,6 +104,30 @@ try {
     assert(result.stdout.includes("update"), "help should mention update subcommand");
     console.log("✓ agent --help shows update subcommand\n");
   }
+
+  // Test 7: agent update accepts thinking as an update field
+  {
+    console.log("Test 7: agent update accepts thinking as an update field");
+    const result =
+      await $`PASEO_HOST=localhost:${port} PASEO_HOME=${paseoHome} npx paseo agent update abc123 --thinking high`.nothrow();
+    const output = result.stdout + result.stderr;
+    assert(!output.includes("Nothing to update"), "should treat --thinking as an update field");
+    console.log("✓ agent update accepts thinking as an update field\n");
+  }
+
+  // Test 8: thinking cannot be combined with metadata updates
+  {
+    console.log("Test 8: thinking cannot be combined with metadata updates");
+    const result =
+      await $`PASEO_HOST=localhost:${port} PASEO_HOME=${paseoHome} npx paseo agent update abc123 --name renamed --thinking high`.nothrow();
+    assert.notStrictEqual(result.exitCode, 0, "should reject a combined update");
+    const output = result.stdout + result.stderr;
+    assert(
+      output.includes("--thinking cannot be combined with --name or --label"),
+      "should explain that thinking and metadata updates are separate operations",
+    );
+    console.log("✓ thinking cannot be combined with metadata updates\n");
+  }
 } finally {
   // Clean up temp directory
   await rm(paseoHome, { recursive: true, force: true });
diff --git a/packages/cli/tests/31-loop-schedule.test.ts b/packages/cli/tests/31-loop-schedule.test.ts
index ae070f8fc..0120ffea6 100644
--- a/packages/cli/tests/31-loop-schedule.test.ts
+++ b/packages/cli/tests/31-loop-schedule.test.ts
@@ -100,6 +100,8 @@ try {
         "10m",
         "--provider",
         "codex/gpt-5.4",
+        "--thinking",
+        "high",
         "--json",
       ],
       { timeout: 30000 },
@@ -113,6 +115,7 @@ try {
     const inspectedJson = JSON.parse(inspected.stdout);
     assert.strictEqual(inspectedJson.target.config.provider, "codex");
     assert.strictEqual(inspectedJson.target.config.model, "gpt-5.4");
+    assert.strictEqual(inspectedJson.target.config.thinkingOptionId, "high");
 
     const deleted = await ctx.paseo(["schedule", "delete", createdJson.id, "--json"]);
     assert.strictEqual(deleted.exitCode, 0, deleted.stderr);
diff --git a/packages/protocol/src/messages.project-command-center.test.ts b/packages/protocol/src/messages.project-command-center.test.ts
index b603162d9..e316b0421 100644
--- a/packages/protocol/src/messages.project-command-center.test.ts
+++ b/packages/protocol/src/messages.project-command-center.test.ts
@@ -168,4 +168,14 @@ describe("project command-center protocol", () => {
     expect(parsed.features?.projectGithubClone).toBeUndefined();
     expect(parsed.features?.projectCreateDirectory).toBeUndefined();
   });
+
+  it("parses the agent thinking update capability", () => {
+    const parsed = parseServerInfoStatusPayload({
+      status: "server_info",
+      serverId: "server-new",
+      features: { agentThinkingUpdate: true },
+    });
+
+    expect(parsed.features?.agentThinkingUpdate).toBe(true);
+  });
 });
diff --git a/packages/protocol/src/messages.ts b/packages/protocol/src/messages.ts
index 5efa8f6a7..dd9772e5c 100644
--- a/packages/protocol/src/messages.ts
+++ b/packages/protocol/src/messages.ts
@@ -2792,6 +2792,8 @@ export const ServerInfoStatusPayloadSchema = z
         providerUsageList: z.boolean().optional(),
         // COMPAT(agentDetach): added in v0.1.98, remove gate after 2026-12-19 once daemon floor >= v0.1.98.
         agentDetach: z.boolean().optional(),
+        // COMPAT(agentThinkingUpdate): added in v0.2.4, remove gate after 2027-01-28.
+        agentThinkingUpdate: z.boolean().optional(),
         // COMPAT(daemonDiagnostics): added in v0.1.100, remove gate after 2026-12-25 once daemon floor >= v0.1.100.
         daemonDiagnostics: z.boolean().optional(),
         // COMPAT(daemonSelfUpdate): added in v0.1.93, remove gate after 2026-12-13.
diff --git a/packages/server/src/server/websocket-server.ts b/packages/server/src/server/websocket-server.ts
index c54c4c5fc..9501fe863 100644
--- a/packages/server/src/server/websocket-server.ts
+++ b/packages/server/src/server/websocket-server.ts
@@ -1540,6 +1540,8 @@ export class VoiceAssistantWebSocketServer {
         providerUsageList: true,
         // COMPAT(agentDetach): added in v0.1.98, remove gate after 2026-12-19 once daemon floor >= v0.1.98.
         agentDetach: true,
+        // COMPAT(agentThinkingUpdate): added in v0.2.4, remove gate after 2027-01-28.
+        agentThinkingUpdate: true,
         // COMPAT(daemonDiagnostics): added in v0.1.100, remove gate after 2026-12-25 once daemon floor >= v0.1.100.
         daemonDiagnostics: true,
         // COMPAT(daemonSelfUpdate): added in v0.1.93, remove gate after 2026-12-13.