diff --git a/openpype/settings/lib.py b/openpype/settings/lib.py
index 60a51c01a0..895fc1e133 100644
--- a/openpype/settings/lib.py
+++ b/openpype/settings/lib.py
@@ -645,13 +645,22 @@ def apply_local_settings_on_project_settings(
         sync_server_config["remote_site"] = remote_site
 
 
-def get_system_settings(clear_metadata=True):
+def get_system_settings(clear_metadata=True, exclude_locals=None):
     """System settings with applied studio overrides."""
     default_values = get_default_settings()[SYSTEM_SETTINGS_KEY]
     studio_values = get_studio_system_settings_overrides()
     result = apply_overrides(default_values, studio_values)
+
+    # Clear overrides metadata from settings
     if clear_metadata:
         clear_metadata_from_settings(result)
+
+    # Apply local settings
+    # Default behavior is based on `clear_metadata` value
+    if exclude_locals is None:
+        exclude_locals = not clear_metadata
+
+    if not exclude_locals:
         # TODO local settings may be required to apply for environments
         local_settings = get_local_settings()
         apply_local_settings_on_system_settings(result, local_settings)
@@ -659,40 +668,52 @@ def get_system_settings(clear_metadata=True):
     return result
 
 
-def get_default_project_settings(clear_metadata=True, exclude_locals=False):
+def get_default_project_settings(clear_metadata=True, exclude_locals=None):
     """Project settings with applied studio's default project overrides."""
     default_values = get_default_settings()[PROJECT_SETTINGS_KEY]
     studio_values = get_studio_project_settings_overrides()
     result = apply_overrides(default_values, studio_values)
+    # Clear overrides metadata from settings
     if clear_metadata:
         clear_metadata_from_settings(result)
-        if not exclude_locals:
-            local_settings = get_local_settings()
-            apply_local_settings_on_project_settings(
-                result, local_settings, None
-            )
+
+    # Apply local settings
+    if exclude_locals is None:
+        exclude_locals = not clear_metadata
+
+    if not exclude_locals:
+        local_settings = get_local_settings()
+        apply_local_settings_on_project_settings(
+            result, local_settings, None
+        )
     return result
 
 
-def get_default_anatomy_settings(clear_metadata=True, exclude_locals=False):
+def get_default_anatomy_settings(clear_metadata=True, exclude_locals=None):
     """Project anatomy data with applied studio's default project overrides."""
     default_values = get_default_settings()[PROJECT_ANATOMY_KEY]
     studio_values = get_studio_project_anatomy_overrides()
 
-    # TODO uncomment and remove hotfix result when overrides of anatomy
-    #   are stored correctly.
     result = apply_overrides(default_values, studio_values)
+    # Clear overrides metadata from settings
     if clear_metadata:
         clear_metadata_from_settings(result)
-        if not exclude_locals:
-            local_settings = get_local_settings()
-            apply_local_settings_on_anatomy_settings(
-                result, local_settings, None
-            )
+
+    # Apply local settings
+    if exclude_locals is None:
+        exclude_locals = not clear_metadata
+
+    if not exclude_locals:
+        local_settings = get_local_settings()
+        apply_local_settings_on_anatomy_settings(
+            result, local_settings, None
+        )
     return result
 
 
-def get_anatomy_settings(project_name, site_name=None, exclude_locals=False):
+def get_anatomy_settings(
+    project_name, site_name=None, clear_metadata=True, exclude_locals=None
+):
     """Project anatomy data with applied studio and project overrides."""
     if not project_name:
         raise ValueError(
@@ -709,7 +730,13 @@ def get_anatomy_settings(project_name, site_name=None, exclude_locals=False):
         for key, value in project_overrides.items():
             result[key] = value
 
-    clear_metadata_from_settings(result)
+    # Clear overrides metadata from settings
+    if clear_metadata:
+        clear_metadata_from_settings(result)
+
+    # Apply local settings
+    if exclude_locals is None:
+        exclude_locals = not clear_metadata
 
     if not exclude_locals:
         local_settings = get_local_settings()
@@ -719,7 +746,9 @@ def get_anatomy_settings(project_name, site_name=None, exclude_locals=False):
     return result
 
 
-def get_project_settings(project_name, exclude_locals=False):
+def get_project_settings(
+    project_name, clear_metadata=True, exclude_locals=None
+):
     """Project settings with applied studio and project overrides."""
     if not project_name:
         raise ValueError(
@@ -733,7 +762,14 @@ def get_project_settings(project_name, exclude_locals=False):
     )
 
     result = apply_overrides(studio_overrides, project_overrides)
-    clear_metadata_from_settings(result)
+
+    # Clear overrides metadata from settings
+    if clear_metadata:
+        clear_metadata_from_settings(result)
+
+    # Apply local settings
+    if exclude_locals is None:
+        exclude_locals = not clear_metadata
 
     if not exclude_locals:
         local_settings = get_local_settings()