diff --git a/openpype/lib/avalon_context.py b/openpype/lib/avalon_context.py
index c4217cc6d5..9695e1e89a 100644
--- a/openpype/lib/avalon_context.py
+++ b/openpype/lib/avalon_context.py
@@ -91,6 +91,10 @@ def create_project(
     #   and Anatomy
     try:
         project_settings_entity = ProjectSettings(project_name)
+        # Remove project overrides will set all anatomy values to defaults
+        # - anatomy will still be overriden
+        project_anatomy = project_settings_entity["project_anatomy"]
+        project_anatomy.remove_from_project_override()
         project_settings_entity.save()
     except SaveWarningExc as exc:
         print(str(exc))