diff --git a/.gitignore b/.gitignore
index b0abe3140b1..1efce4b83f1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -108,6 +108,12 @@ docs/superpowers/*
 # logs, and per-session caches are never artifacts of the codebase.
 .hermes/
 
+# Desktop/bootstrap install marker written into the managed checkout root by the
+# bootstrap installer. It is Hermes-managed runtime state, never a code change —
+# ignore it so `hermes update`'s `git stash push --include-untracked` does not
+# treat it as a local edit and autostash it on every run (#38529).
+.hermes-bootstrap-complete
+
 # Tool Search live-test harness output — non-deterministic model transcripts,
 # regenerated by scripts/tool_search_livetest.py. Never an artifact of the repo.
 scripts/out/
diff --git a/tests/hermes_cli/test_update_autostash.py b/tests/hermes_cli/test_update_autostash.py
index 3ba19965591..16946834ab1 100644
--- a/tests/hermes_cli/test_update_autostash.py
+++ b/tests/hermes_cli/test_update_autostash.py
@@ -819,3 +819,50 @@ def test_cmd_update_skips_stash_restore_when_reset_fails(monkeypatch, tmp_path,
 
     out = capsys.readouterr().out
     assert "preserved in stash" in out
+
+
+def test_bootstrap_marker_not_autostashed_by_update(tmp_path):
+    """#38529: the Desktop bootstrap marker must be git-ignored so that
+    ``hermes update``'s ``git stash push --include-untracked`` does not sweep it
+    into an autostash on every run.
+
+    Behavioral + hermetic: build a throwaway repo that adopts the project's real
+    ``.gitignore`` (the contract under test), drop the marker, and confirm the
+    same stash invocation the updater uses leaves it untouched.
+    """
+    import shutil
+    import subprocess
+
+    if shutil.which("git") is None:
+        pytest.skip("git not available")
+
+    repo_gitignore = Path(hermes_main.__file__).resolve().parents[1] / ".gitignore"
+
+    def git(*args):
+        return subprocess.run(
+            ["git", *args], cwd=tmp_path, capture_output=True, text=True, check=True
+        )
+
+    git("init", "-q")
+    git("config", "user.email", "t@example.com")
+    git("config", "user.name", "t")
+    (tmp_path / ".gitignore").write_text(repo_gitignore.read_text())
+    (tmp_path / "tracked.txt").write_text("x\n")
+    git("add", "-A")
+    git("commit", "-qm", "init")
+
+    marker = tmp_path / ".hermes-bootstrap-complete"
+    marker.write_text("")
+
+    # Exact flags used by hermes update (hermes_cli/main.py).
+    git("stash", "push", "--include-untracked", "-m", "hermes-update-autostash")
+
+    assert marker.exists(), (
+        ".hermes-bootstrap-complete was swept into the update autostash — it must "
+        "be listed in .gitignore so `git stash -u` skips it (#38529)."
+    )
+    # It must not even register as a dirty/untracked change.
+    status = subprocess.run(
+        ["git", "status", "--porcelain"], cwd=tmp_path, capture_output=True, text=True
+    ).stdout
+    assert ".hermes-bootstrap-complete" not in status