diff --git a/cli/code_scanner.py b/cli/code_scanner.py
index 193f4049..58768937 100644
--- a/cli/code_scanner.py
+++ b/cli/code_scanner.py
@@ -18,6 +18,7 @@
 from cli.config import configuration_manager
 from cli.utils.path_utils import is_sub_path, is_binary_file, get_file_size, get_relevant_files_in_path, get_path_by_os
 from cli.utils.string_utils import get_content_size, is_binary_content
+from cli.user_settings.config_file_manager import ConfigFileManager
 from cli.zip_file import InMemoryZip
 from cli.exceptions.custom_exceptions import CycodeError, HttpUnauthorizedError, ZipTooLargeError
 from cyclient import logger
@@ -398,7 +399,8 @@ def _does_document_exceed_max_size_limit(content: str) -> bool:
 
 def _is_subpath_of_cycode_configuration_folder(filename: str) -> bool:
     return is_sub_path(configuration_manager.global_config_file_manager.get_config_directory_path(), filename) \
-           or is_sub_path(configuration_manager.local_config_file_manager.get_config_directory_path(), filename)
+           or is_sub_path(configuration_manager.local_config_file_manager.get_config_directory_path(), filename) \
+           or filename.endswith(ConfigFileManager.get_config_file_route())
 
 
 def _handle_exception(context: click.Context, e: Exception):
diff --git a/cli/user_settings/config_file_manager.py b/cli/user_settings/config_file_manager.py
index 91f437e4..e3503693 100644
--- a/cli/user_settings/config_file_manager.py
+++ b/cli/user_settings/config_file_manager.py
@@ -63,6 +63,10 @@ def get_config_directory_path(self) -> str:
     def get_filename(self) -> str:
         return os.path.join(self.get_config_directory_path(), self.FILE_NAME)
 
+    @staticmethod
+    def get_config_file_route() -> str:
+        return os.path.join(ConfigFileManager.CYCODE_HIDDEN_DIRECTORY, ConfigFileManager.FILE_NAME)
+
     def _get_exclusions_by_exclusion_type(self, scan_type, exclusion_type) -> List:
         scan_type_exclusions = self.get_exclusions_by_scan_type(scan_type)
         return scan_type_exclusions.get(exclusion_type, [])