diff --git a/python/extractor/cli-integration-test/hidden-files/config.yml b/python/extractor/cli-integration-test/hidden-files/config.yml
new file mode 100644
index 00000000000..69d94597d95
--- /dev/null
+++ b/python/extractor/cli-integration-test/hidden-files/config.yml
@@ -0,0 +1,3 @@
+name: Test Config
+paths-ignore:
+  - "**/.*/**"
diff --git a/python/extractor/cli-integration-test/hidden-files/query-default.expected b/python/extractor/cli-integration-test/hidden-files/query-default.expected
index cc92af624b3..72d34a1ab0b 100644
--- a/python/extractor/cli-integration-test/hidden-files/query-default.expected
+++ b/python/extractor/cli-integration-test/hidden-files/query-default.expected
@@ -1,5 +1,6 @@
 |             name              |
 +-------------------------------+
 | .hidden_file.py               |
+| another_non_hidden.py         |
 | foo.py                        |
 | visible_file_in_hidden_dir.py |
diff --git a/python/extractor/cli-integration-test/hidden-files/repo_dir/.hidden_dir/internal_non_hidden/another_non_hidden.py b/python/extractor/cli-integration-test/hidden-files/repo_dir/.hidden_dir/internal_non_hidden/another_non_hidden.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/python/extractor/cli-integration-test/hidden-files/test.sh b/python/extractor/cli-integration-test/hidden-files/test.sh
index 77cb12664af..45485985adb 100755
--- a/python/extractor/cli-integration-test/hidden-files/test.sh
+++ b/python/extractor/cli-integration-test/hidden-files/test.sh
@@ -16,8 +16,8 @@ $CODEQL database create db --language python --source-root repo_dir/
 $CODEQL query run --database db query.ql > query-default.actual
 diff query-default.expected query-default.actual
 
-# Test 2: Setting the relevant extractor option to true skips files in hidden directories
-$CODEQL database create db-skipped --language python --source-root repo_dir/ --extractor-option python.skip_hidden_directories=true
+# Test 2: The default behavior can be overridden by setting `paths-ignore` in the config file
+$CODEQL database create db-skipped --language python --source-root repo_dir/ --codescanning-config=config.yml
 $CODEQL query run --database db-skipped query.ql > query-skipped.actual
 diff query-skipped.expected query-skipped.actual