diff --git a/editor/editor_node.cpp b/editor/editor_node.cpp
index f307d463a4b..9c150446c72 100644
--- a/editor/editor_node.cpp
+++ b/editor/editor_node.cpp
@@ -514,8 +514,10 @@ void EditorNode::_notification(int p_what) {
 
 			_update_debug_options();
 
-			// Save the project after opening to mark it as last modified.
-			ProjectSettings::get_singleton()->save();
+			// Save the project after opening to mark it as last modified, except in headless mode.
+			if (OS::get_singleton()->can_draw() && !OS::get_singleton()->is_no_window_mode_enabled()) {
+				ProjectSettings::get_singleton()->save();
+			}
 
 			/* DO NOT LOAD SCENES HERE, WAIT FOR FILE SCANNING AND REIMPORT TO COMPLETE */
 		} break;