diff --git a/editor/editor_file_system.cpp b/editor/editor_file_system.cpp
index b6d1b92f9f68..e81f71e0e09e 100644
--- a/editor/editor_file_system.cpp
+++ b/editor/editor_file_system.cpp
@@ -2369,7 +2369,9 @@ bool EditorFileSystem::_should_skip_directory(const String &p_path) {
 
 	if (FileAccess::exists(p_path.path_join("project.godot"))) {
 		// Skip if another project inside this.
-		WARN_PRINT_ONCE(vformat("Detected another project.godot at %s. The folder will be ignored.", p_path));
+		if (EditorFileSystem::get_singleton()->first_scan) {
+			WARN_PRINT_ONCE(vformat("Detected another project.godot at %s. The folder will be ignored.", p_path));
+		}
 		return true;
 	}