diff --git a/frappe/modules/utils.py b/frappe/modules/utils.py
index 1f89dae716..b8ab6756a5 100644
--- a/frappe/modules/utils.py
+++ b/frappe/modules/utils.py
@@ -105,17 +105,12 @@ def sync_customizations(app: Optional[str] = None):
 	apps = frappe.get_installed_apps() if not app else [app]
 
 	for app_name in apps:
-		for module_name in frappe.local.app_modules.get(app_name) or []:
-			module_custom_folder = frappe.get_app_path(app_name, module_name, "custom")
-			if not os.path.exists(module_custom_folder):
-				continue
+		for json_file in glob(frappe.get_app_path(app_name, "**", "custom", "*.json")):
+			with open(json_file, "r") as f:
+				data = json.loads(f.read())
 
-			for json_file in glob(os.path.join(module_custom_folder, "*.json")):
-				with open(os.path.join(module_custom_folder, json_file), "r") as f:
-					data = json.loads(f.read())
-
-				if data.get("sync_on_migrate"):
-					sync_customizations_for_doctype(data, module_custom_folder)
+			if data.get("sync_on_migrate"):
+				sync_customizations_for_doctype(data, os.path.dirname(json_file))
 
 
 def sync_customizations_for_doctype(data: Dict, folder: str):