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;