diff --git a/src/resources/extensions/gsd/bootstrap/system-context.ts b/src/resources/extensions/gsd/bootstrap/system-context.ts
index 8fe3890df..bad24512d 100644
--- a/src/resources/extensions/gsd/bootstrap/system-context.ts
+++ b/src/resources/extensions/gsd/bootstrap/system-context.ts
@@ -19,6 +19,7 @@ import { deriveState } from "../state.js";
 import { formatOverridesSection, formatShortcut, loadActiveOverrides, loadFile, parseContinue, parseSummary } from "../files.js";
 import { toPosixPath } from "../../shared/mod.js";
 import { markCmuxPromptShown, shouldPromptToEnableCmux } from "../../cmux/index.js";
+import { autoEnableCmuxPreferences } from "../commands-cmux.js";
 
 const gsdHome = process.env.GSD_HOME || join(homedir(), ".gsd");
 
@@ -76,13 +77,16 @@ export async function buildBeforeAgentStartResult(
     shortcutDashboard: formatShortcut("Ctrl+Alt+G"),
     shortcutShell: formatShortcut("Ctrl+Alt+B"),
   });
-  const loadedPreferences = loadEffectiveGSDPreferences();
+  let loadedPreferences = loadEffectiveGSDPreferences();
   if (shouldPromptToEnableCmux(loadedPreferences?.preferences)) {
     markCmuxPromptShown();
-    ctx.ui.notify(
-      "cmux detected. Run /gsd cmux on to enable sidebar metadata, notifications, and visual subagent splits for this project.",
-      "info",
-    );
+    if (autoEnableCmuxPreferences()) {
+      loadedPreferences = loadEffectiveGSDPreferences();
+      ctx.ui.notify(
+        "cmux detected — auto-enabled. Run /gsd cmux off to disable.",
+        "info",
+      );
+    }
   }
 
   let preferenceBlock = "";
diff --git a/src/resources/extensions/gsd/commands-cmux.ts b/src/resources/extensions/gsd/commands-cmux.ts
index e00f2dea2..a1b8f5ee4 100644
--- a/src/resources/extensions/gsd/commands-cmux.ts
+++ b/src/resources/extensions/gsd/commands-cmux.ts
@@ -1,5 +1,5 @@
 import type { ExtensionCommandContext } from "@gsd/pi-coding-agent";
-import { existsSync, readFileSync } from "node:fs";
+import { existsSync, readFileSync, writeFileSync } from "node:fs";
 import { clearCmuxSidebar, CmuxClient, detectCmuxEnvironment, resolveCmuxConfig } from "../cmux/index.js";
 import { saveFile } from "./files.js";
 import {
@@ -9,6 +9,37 @@ import {
 } from "./preferences.js";
 import { ensurePreferencesFile, serializePreferencesToFrontmatter } from "./commands-prefs-wizard.js";
 
+/**
+ * Auto-enable cmux in project preferences when detected but never configured.
+ * Called at boot (before agent start) — no ExtensionCommandContext needed.
+ * Returns true if preferences were written, false if skipped.
+ */
+export function autoEnableCmuxPreferences(): boolean {
+  const path = getProjectGSDPreferencesPath();
+  if (!existsSync(path)) return false;
+
+  const existing = loadProjectGSDPreferences();
+  const prefs: Record<string, unknown> = existing?.preferences ? { ...existing.preferences } : { version: 1 };
+  prefs.cmux = {
+    enabled: true,
+    notifications: true,
+    sidebar: true,
+    splits: false,
+    browser: false,
+    ...((prefs.cmux as Record<string, unknown> | undefined) ?? {}),
+  };
+  (prefs.cmux as Record<string, unknown>).enabled = true;
+  prefs.version = prefs.version || 1;
+
+  const frontmatter = serializePreferencesToFrontmatter(prefs);
+  let body = "\n# GSD Skill Preferences\n\nSee `~/.gsd/agent/extensions/gsd/docs/preferences-reference.md` for full field documentation and examples.\n";
+  const preserved = extractBodyAfterFrontmatter(readFileSync(path, "utf-8"));
+  if (preserved) body = preserved;
+
+  writeFileSync(path, `---\n${frontmatter}---${body}`, "utf-8");
+  return true;
+}
+
 function extractBodyAfterFrontmatter(content: string): string | null {
   const start = content.startsWith("---\n") ? 4 : content.startsWith("---\r\n") ? 5 : -1;
   if (start === -1) return null;
diff --git a/src/resources/extensions/gsd/tests/cmux.test.ts b/src/resources/extensions/gsd/tests/cmux.test.ts
index 0e6dd8e77..305a3ef0d 100644
--- a/src/resources/extensions/gsd/tests/cmux.test.ts
+++ b/src/resources/extensions/gsd/tests/cmux.test.ts
@@ -1,7 +1,8 @@
-import test, { describe } from "node:test";
+import test, { describe, beforeEach, afterEach } from "node:test";
 import assert from "node:assert/strict";
 import * as fs from "node:fs";
 import * as path from "node:path";
+import { tmpdir } from "node:os";
 import { fileURLToPath } from "node:url";
 import {
   buildCmuxProgress,
@@ -12,6 +13,7 @@ import {
   resolveCmuxConfig,
   shouldPromptToEnableCmux,
 } from "../../cmux/index.ts";
+import { autoEnableCmuxPreferences } from "../commands-cmux.ts";
 import type { GSDState } from "../types.ts";
 
 test("detectCmuxEnvironment requires workspace, surface, and socket", () => {
@@ -79,6 +81,70 @@ test("shouldPromptToEnableCmux only prompts once per session", () => {
   resetCmuxPromptState();
 });
 
+describe("autoEnableCmuxPreferences", () => {
+  let tmp: string;
+  let originalCwd: string;
+
+  beforeEach(() => {
+    originalCwd = process.cwd();
+    tmp = fs.mkdtempSync(path.join(tmpdir(), "cmux-auto-test-"));
+    fs.mkdirSync(path.join(tmp, ".gsd"), { recursive: true });
+    process.chdir(tmp);
+  });
+
+  afterEach(() => {
+    process.chdir(originalCwd);
+    fs.rmSync(tmp, { recursive: true, force: true });
+  });
+
+  test("writes cmux.enabled true when preferences file exists with no cmux config", () => {
+    const prefsPath = path.join(tmp, ".gsd", "preferences.md");
+    fs.writeFileSync(prefsPath, [
+      "---",
+      "version: 1",
+      "---",
+      "",
+      "# GSD Skill Preferences",
+    ].join("\n"));
+
+    const result = autoEnableCmuxPreferences();
+    assert.equal(result, true);
+
+    const content = fs.readFileSync(prefsPath, "utf-8");
+    assert.ok(content.includes("enabled: true"), "should write enabled: true");
+    assert.ok(content.includes("notifications: true"), "should default notifications on");
+    assert.ok(content.includes("sidebar: true"), "should default sidebar on");
+    assert.ok(content.includes("splits: false"), "should default splits off");
+  });
+
+  test("returns false when preferences file does not exist", () => {
+    const result = autoEnableCmuxPreferences();
+    assert.equal(result, false);
+  });
+
+  test("preserves existing cmux sub-preferences when auto-enabling", () => {
+    const prefsPath = path.join(tmp, ".gsd", "preferences.md");
+    fs.writeFileSync(prefsPath, [
+      "---",
+      "version: 1",
+      "cmux:",
+      "  splits: true",
+      "  browser: true",
+      "---",
+      "",
+      "# GSD Skill Preferences",
+    ].join("\n"));
+
+    const result = autoEnableCmuxPreferences();
+    assert.equal(result, true);
+
+    const content = fs.readFileSync(prefsPath, "utf-8");
+    assert.ok(content.includes("enabled: true"), "should set enabled: true");
+    assert.ok(content.includes("splits: true"), "should preserve existing splits: true");
+    assert.ok(content.includes("browser: true"), "should preserve existing browser: true");
+  });
+});
+
 test("buildCmuxStatusLabel and progress prefer deepest active unit", () => {
   const state: GSDState = {
     activeMilestone: { id: "M001", title: "Milestone" },