diff --git a/editor/editor_file_system.cpp b/editor/editor_file_system.cpp
index 7840645a9d4..e13a9842138 100644
--- a/editor/editor_file_system.cpp
+++ b/editor/editor_file_system.cpp
@@ -1896,7 +1896,12 @@ void EditorFileSystem::_update_script_classes() {
 
 		EditorProgress *ep = nullptr;
 		if (update_script_paths.size() > 1) {
-			ep = memnew(EditorProgress("update_scripts_classes", TTR("Registering global classes..."), update_script_paths.size()));
+			if (MessageQueue::get_singleton()->is_flushing()) {
+				// Use background progress when message queue is flushing.
+				ep = memnew(EditorProgress("update_scripts_classes", TTR("Registering global classes..."), update_script_paths.size(), false, true));
+			} else {
+				ep = memnew(EditorProgress("update_scripts_classes", TTR("Registering global classes..."), update_script_paths.size()));
+			}
 		}
 
 		int step_count = 0;
@@ -1935,7 +1940,12 @@ void EditorFileSystem::_update_script_documentation() {
 
 	EditorProgress *ep = nullptr;
 	if (update_script_paths_documentation.size() > 1) {
-		ep = memnew(EditorProgress("update_script_paths_documentation", TTR("Updating scripts documentation"), update_script_paths_documentation.size()));
+		if (MessageQueue::get_singleton()->is_flushing()) {
+			// Use background progress when message queue is flushing.
+			ep = memnew(EditorProgress("update_script_paths_documentation", TTR("Updating scripts documentation"), update_script_paths_documentation.size(), false, true));
+		} else {
+			ep = memnew(EditorProgress("update_script_paths_documentation", TTR("Updating scripts documentation"), update_script_paths_documentation.size()));
+		}
 	}
 
 	int step_count = 0;
diff --git a/editor/editor_node.cpp b/editor/editor_node.cpp
index 47b5fa4d1a2..f154cbd1e2a 100644
--- a/editor/editor_node.cpp
+++ b/editor/editor_node.cpp
@@ -175,7 +175,7 @@ static const String REMOVE_ANDROID_BUILD_TEMPLATE_MESSAGE = "The Android build t
 static const String INSTALL_ANDROID_BUILD_TEMPLATE_MESSAGE = "This will set up your project for gradle Android builds by installing the source template to \"%s\".\nNote that in order to make gradle builds instead of using pre-built APKs, the \"Use Gradle Build\" option should be enabled in the Android export preset.";
 
 bool EditorProgress::step(const String &p_state, int p_step, bool p_force_refresh) {
-	if (Thread::is_main_thread()) {
+	if (!force_background && Thread::is_main_thread()) {
 		return EditorNode::progress_task_step(task, p_state, p_step, p_force_refresh);
 	} else {
 		EditorNode::progress_task_step_bg(task, p_step);
@@ -183,17 +183,18 @@ bool EditorProgress::step(const String &p_state, int p_step, bool p_force_refres
 	}
 }
 
-EditorProgress::EditorProgress(const String &p_task, const String &p_label, int p_amount, bool p_can_cancel) {
-	if (Thread::is_main_thread()) {
+EditorProgress::EditorProgress(const String &p_task, const String &p_label, int p_amount, bool p_can_cancel, bool p_force_background) {
+	if (!p_force_background && Thread::is_main_thread()) {
 		EditorNode::progress_add_task(p_task, p_label, p_amount, p_can_cancel);
 	} else {
 		EditorNode::progress_add_task_bg(p_task, p_label, p_amount);
 	}
 	task = p_task;
+	force_background = p_force_background;
 }
 
 EditorProgress::~EditorProgress() {
-	if (Thread::is_main_thread()) {
+	if (!force_background && Thread::is_main_thread()) {
 		EditorNode::progress_end_task(task);
 	} else {
 		EditorNode::progress_end_task_bg(task);
diff --git a/editor/editor_node.h b/editor/editor_node.h
index bdf9b26a7ac..e24bae73f0b 100644
--- a/editor/editor_node.h
+++ b/editor/editor_node.h
@@ -124,9 +124,10 @@ class WindowWrapper;
 
 struct EditorProgress {
 	String task;
+	bool force_background = false;
 	bool step(const String &p_state, int p_step = -1, bool p_force_refresh = true);
 
-	EditorProgress(const String &p_task, const String &p_label, int p_amount, bool p_can_cancel = false);
+	EditorProgress(const String &p_task, const String &p_label, int p_amount, bool p_can_cancel = false, bool p_force_background = false);
 	~EditorProgress();
 };