diff --git a/docker/run/AGENTS.md b/docker/run/AGENTS.md
index 9077e5a90..b5607ae69 100644
--- a/docker/run/AGENTS.md
+++ b/docker/run/AGENTS.md
@@ -22,6 +22,7 @@
 - Do not bake secrets, local `.env` values, or user data into the image.
 - Runtime startup must ensure `/a0/usr/uploads` exists before supervised services start.
 - Runtime startup raises the soft open-file limit toward `A0_NOFILE_LIMIT` (default `65535`) before supervisord starts, bounded by the container hard limit.
+- Self-update user-data backups skip Time Travel shadow history under `usr/.time_travel/` and transient Desktop agent state.
 
 ## Work Guidance
 
diff --git a/docker/run/fs/exe/self_update_manager.py b/docker/run/fs/exe/self_update_manager.py
index abf4e595f..4ae23ce28 100644
--- a/docker/run/fs/exe/self_update_manager.py
+++ b/docker/run/fs/exe/self_update_manager.py
@@ -405,6 +405,11 @@ def should_exclude_from_usr_backup(
     logger: AttemptLogger,
 ) -> bool:
     parts = relative_dir.parts
+    if parts and parts[0] == ".time_travel":
+        logger.log(
+            f"Skipping Time Travel history during usr backup: {Path('usr') / relative_dir}"
+        )
+        return True
     if (
         len(parts) >= 6
         and parts[0] == "plugins"
diff --git a/helpers/backup.py b/helpers/backup.py
index 47e41c5f8..70ad7b082 100644
--- a/helpers/backup.py
+++ b/helpers/backup.py
@@ -63,6 +63,7 @@ class BackupService:
         return f"""# User data
 # All persistent user data is now centralized in /usr for easier backup and restore
 {agent_root}/usr/**
+!{agent_root}/usr/.time_travel/**
 """
 
     def _get_agent_zero_version(self) -> str:
diff --git a/helpers/backup.py.dox.md b/helpers/backup.py.dox.md
index e08f7a74e..5612447ec 100644
--- a/helpers/backup.py.dox.md
+++ b/helpers/backup.py.dox.md
@@ -26,6 +26,7 @@
 - Observed side-effect areas: filesystem reads, filesystem writes, filesystem deletion, settings/state persistence, secret handling.
 - Imported dependency areas include: `datetime`, `helpers`, `helpers.localization`, `helpers.print_style`, `json`, `os`, `pathspec`, `platform`, `tempfile`, `typing`, `zipfile`.
 - `test_patterns(..., max_files=None)` is the unlimited scan mode. UI preview and dry-run callers may pass bounded limits, but real backup creation and restore clean-before-restore must use unlimited matching so archives and cleanup are not silently truncated.
+- Default backup metadata includes persistent `/usr` data but excludes Time Travel shadow history under `usr/.time_travel/**`.
 
 ## Key Concepts
 
diff --git a/tests/test_backup_large_archives.py b/tests/test_backup_large_archives.py
index 7638fbbc5..e8c607655 100644
--- a/tests/test_backup_large_archives.py
+++ b/tests/test_backup_large_archives.py
@@ -16,6 +16,28 @@ class UploadedBackup:
         shutil.copyfile(self.path, target)
 
 
+@pytest.mark.asyncio
+async def test_default_backup_patterns_exclude_time_travel_history(tmp_path):
+    root = tmp_path / "a0"
+    usr = root / "usr"
+    time_travel = usr / ".time_travel" / "workspaces" / "demo" / "repo.git"
+    time_travel.mkdir(parents=True)
+    (usr / "settings.json").write_text('{"ok": true}\n', encoding="utf-8")
+    (time_travel / "objects.pack").write_text("history\n", encoding="utf-8")
+
+    service = BackupService()
+    service.agent_zero_root = str(root)
+    service.base_paths = {str(root): str(root)}
+    metadata = service.get_default_backup_metadata()
+
+    files = await service.test_patterns(metadata, max_files=None)
+    paths = {item["real_path"] for item in files}
+
+    assert str(usr / "settings.json") in paths
+    assert str(time_travel / "objects.pack") not in paths
+    assert f"{root}/usr/.time_travel/**" in metadata["exclude_patterns"]
+
+
 @pytest.mark.asyncio
 async def test_pattern_scan_can_run_without_file_limit(tmp_path):
     root = tmp_path / "a0"
diff --git a/tests/test_self_update_tag_filter.py b/tests/test_self_update_tag_filter.py
index 864a471e5..2f351f4ad 100644
--- a/tests/test_self_update_tag_filter.py
+++ b/tests/test_self_update_tag_filter.py
@@ -829,6 +829,39 @@ def test_self_update_manager_usr_backup_skips_runtime_sockets():
         )
 
 
+def test_self_update_manager_usr_backup_skips_time_travel_history(tmp_path):
+    manager = load_self_update_manager()
+    repo_dir = tmp_path / "repo"
+    usr_dir = repo_dir / "usr"
+    time_travel = usr_dir / ".time_travel" / "workspaces" / "demo" / "repo.git"
+    time_travel.mkdir(parents=True)
+    (usr_dir / "settings.json").write_text('{"ok": true}\n', encoding="utf-8")
+    (time_travel / "objects.pack").write_text("history\n", encoding="utf-8")
+    messages = []
+
+    class ListLogger:
+        def log(self, message=""):
+            messages.append(message)
+
+    backup_path = manager.create_usr_backup(
+        repo_dir=repo_dir,
+        backup_path=str(tmp_path / "backups"),
+        backup_name="usr-backup.zip",
+        conflict_policy="rename",
+        logger=ListLogger(),
+    )
+
+    with zipfile.ZipFile(backup_path) as archive:
+        names = set(archive.namelist())
+
+    assert "usr/settings.json" in names
+    assert "usr/.time_travel/workspaces/demo/repo.git/objects.pack" not in names
+    assert any(
+        "Skipping Time Travel history during usr backup: usr/.time_travel" in message
+        for message in messages
+    )
+
+
 def test_self_update_manager_usr_backup_skips_transient_desktop_ssh_agent_dir(tmp_path):
     manager = load_self_update_manager()
     repo_dir = tmp_path / "repo"