diff --git a/src/pickley/__init__.py b/src/pickley/__init__.py
index e878d9d..8dc67f9 100644
--- a/src/pickley/__init__.py
+++ b/src/pickley/__init__.py
@@ -13,6 +13,7 @@
 from runez.pyenv import PypiStd, PythonDepot, Version
 
 from pickley import bstrap
+from pickley.bstrap import PICKLEY
 
 LOG = logging.getLogger(__name__)
 DEFAULT_VERSION_CHECK_DELAY = 300
@@ -588,6 +589,9 @@ def save_manifest(self):
             manifest.package_manager = venv_settings.package_manager
             manifest.python_executable = venv_settings.python_executable
 
+        if self.canonical_name == PICKLEY:
+            runez.save_json(manifest.install_info, CFG.manifests / ".bootstrap.json")
+
         payload = manifest.to_dict()
         runez.save_json(payload, self.manifest_path)
         folder = self.target_installation_folder()
diff --git a/src/pickley/cli.py b/src/pickley/cli.py
index 61522fa..04ef84e 100644
--- a/src/pickley/cli.py
+++ b/src/pickley/cli.py
@@ -14,7 +14,7 @@
 from runez.pyenv import Version
 from runez.render import PrettyTable
 
-from pickley import bstrap, CFG, PackageSpec, Reporter, ResolvedPackage, TrackedInstallInfo, TrackedSettings
+from pickley import bstrap, CFG, PackageSpec, PICKLEY, Reporter, ResolvedPackage, TrackedSettings
 from pickley.package import VenvPackager
 
 LOG = logging.getLogger(__name__)
@@ -342,7 +342,10 @@ def auto_heal():
 @click.argument("package", required=True)
 def auto_upgrade(force, package):
     """Background auto-upgrade command (called by wrapper)"""
-    CFG.require_bootstrap()
+    if package != PICKLEY:
+        # Auto-upgrade of pickley will mark current installation as bootstrapped
+        CFG.require_bootstrap()
+
     canonical_name = CFG.required_canonical_name(package)
     pspec = PackageSpec(canonical_name)
     cooldown_path = CFG.cache / f"{canonical_name}.cooldown"
@@ -409,7 +412,6 @@ def bootstrap(base_folder, pickley_spec):
 
     pspec = PackageSpec(pickley_spec or bstrap.PICKLEY, authoritative=bool(pickley_spec))
     perform_install(pspec)
-    runez.save_json(TrackedInstallInfo.current(), bootstrap_marker)
 
 
 @main.command()