diff --git a/tools/idf_tools.py b/tools/idf_tools.py
index a928c04656..17617c1505 100755
--- a/tools/idf_tools.py
+++ b/tools/idf_tools.py
@@ -2574,7 +2574,10 @@ def action_install_python_env(args):  # type: ignore
     reinstall = args.reinstall
     idf_python_env_path, _, virtualenv_python, idf_version = get_python_env_path()
 
-    is_virtualenv = hasattr(sys, 'real_prefix') or (hasattr(sys, 'base_prefix') and sys.base_prefix != sys.prefix)
+    nix_store = os.environ.get('NIX_STORE')
+    is_nix = nix_store is not None and sys.base_prefix.startswith(nix_store) and sys.prefix.startswith(nix_store)
+
+    is_virtualenv = not is_nix and (hasattr(sys, 'real_prefix') or (hasattr(sys, 'base_prefix') and sys.base_prefix != sys.prefix))
     if is_virtualenv and (not os.path.exists(idf_python_env_path) or reinstall):
         fatal('This script was called from a virtual environment, can not create a virtual environment again')
         raise SystemExit(1)