diff --git a/editor/dependency_editor.cpp b/editor/dependency_editor.cpp
index 02b0eca6aa6..8ba5811ffa6 100644
--- a/editor/dependency_editor.cpp
+++ b/editor/dependency_editor.cpp
@@ -572,32 +572,34 @@ void DependencyRemoveDialog::ok_pressed() {
 		}
 	}
 
+	bool project_settings_modified = false;
 	for (int i = 0; i < files_to_delete.size(); ++i) {
 		// If the file we are deleting for e.g. the main scene, default environment,
 		// or audio bus layout, we must clear its definition in Project Settings.
 		if (files_to_delete[i] == String(GLOBAL_GET("application/config/icon"))) {
 			ProjectSettings::get_singleton()->set("application/config/icon", "");
-		}
-		if (files_to_delete[i] == String(GLOBAL_GET("application/run/main_scene"))) {
+			project_settings_modified = true;
+		} else if (files_to_delete[i] == String(GLOBAL_GET("application/run/main_scene"))) {
 			ProjectSettings::get_singleton()->set("application/run/main_scene", "");
-		}
-		if (files_to_delete[i] == String(GLOBAL_GET("application/boot_splash/image"))) {
+			project_settings_modified = true;
+		} else if (files_to_delete[i] == String(GLOBAL_GET("application/boot_splash/image"))) {
 			ProjectSettings::get_singleton()->set("application/boot_splash/image", "");
-		}
-		if (files_to_delete[i] == String(GLOBAL_GET("rendering/environment/defaults/default_environment"))) {
+			project_settings_modified = true;
+		} else if (files_to_delete[i] == String(GLOBAL_GET("rendering/environment/defaults/default_environment"))) {
 			ProjectSettings::get_singleton()->set("rendering/environment/defaults/default_environment", "");
-		}
-		if (files_to_delete[i] == String(GLOBAL_GET("display/mouse_cursor/custom_image"))) {
+			project_settings_modified = true;
+		} else if (files_to_delete[i] == String(GLOBAL_GET("display/mouse_cursor/custom_image"))) {
 			ProjectSettings::get_singleton()->set("display/mouse_cursor/custom_image", "");
-		}
-		if (files_to_delete[i] == String(GLOBAL_GET("gui/theme/custom"))) {
+			project_settings_modified = true;
+		} else if (files_to_delete[i] == String(GLOBAL_GET("gui/theme/custom"))) {
 			ProjectSettings::get_singleton()->set("gui/theme/custom", "");
-		}
-		if (files_to_delete[i] == String(GLOBAL_GET("gui/theme/custom_font"))) {
+			project_settings_modified = true;
+		} else if (files_to_delete[i] == String(GLOBAL_GET("gui/theme/custom_font"))) {
 			ProjectSettings::get_singleton()->set("gui/theme/custom_font", "");
-		}
-		if (files_to_delete[i] == String(GLOBAL_GET("audio/buses/default_bus_layout"))) {
+			project_settings_modified = true;
+		} else if (files_to_delete[i] == String(GLOBAL_GET("audio/buses/default_bus_layout"))) {
 			ProjectSettings::get_singleton()->set("audio/buses/default_bus_layout", "");
+			project_settings_modified = true;
 		}
 
 		String path = OS::get_singleton()->get_resource_dir() + files_to_delete[i].replace_first("res://", "/");
@@ -609,6 +611,9 @@ void DependencyRemoveDialog::ok_pressed() {
 			emit_signal(SNAME("file_removed"), files_to_delete[i]);
 		}
 	}
+	if (project_settings_modified) {
+		ProjectSettings::get_singleton()->save();
+	}
 
 	if (dirs_to_delete.size() == 0) {
 		// If we only deleted files we should only need to tell the file system about the files we touched.