diff --git a/scene/gui/menu_button.cpp b/scene/gui/menu_button.cpp
index 622860e777e..ae74936a208 100644
--- a/scene/gui/menu_button.cpp
+++ b/scene/gui/menu_button.cpp
@@ -81,6 +81,10 @@ void MenuButton::show_popup() {
 	emit_signal(SNAME("about_to_popup"));
 	Rect2 rect = get_screen_rect();
 	rect.position.y += rect.size.height;
+	if (get_viewport()->is_embedding_subwindows() && popup->get_force_native()) {
+		Transform2D xform = get_viewport()->get_popup_base_transform_native();
+		rect = xform.xform(rect);
+	}
 	rect.size.height = 0;
 	popup->set_size(rect.size);
 	if (is_layout_rtl()) {
diff --git a/scene/gui/option_button.cpp b/scene/gui/option_button.cpp
index d1a1d21a416..2823ba9c792 100644
--- a/scene/gui/option_button.cpp
+++ b/scene/gui/option_button.cpp
@@ -541,6 +541,10 @@ void OptionButton::show_popup() {
 
 	Rect2 rect = get_screen_rect();
 	rect.position.y += rect.size.height;
+	if (get_viewport()->is_embedding_subwindows() && popup->get_force_native()) {
+		Transform2D xform = get_viewport()->get_popup_base_transform_native();
+		rect = xform.xform(rect);
+	}
 	rect.size.height = 0;
 	popup->popup(rect);
 }
diff --git a/scene/gui/popup_menu.cpp b/scene/gui/popup_menu.cpp
index 52295343938..facd4aa4386 100644
--- a/scene/gui/popup_menu.cpp
+++ b/scene/gui/popup_menu.cpp
@@ -3216,7 +3216,7 @@ void PopupMenu::popup(const Rect2i &p_bounds) {
 }
 
 void PopupMenu::_pre_popup() {
-	Size2 scale = get_parent_viewport()->get_popup_base_transform().get_scale();
+	Size2 scale = get_force_native() ? get_parent_viewport()->get_popup_base_transform_native().get_scale() : get_parent_viewport()->get_popup_base_transform().get_scale();
 	CanvasItem *c = Object::cast_to<CanvasItem>(get_parent());
 	if (c) {
 		scale *= c->get_global_transform_with_canvas().get_scale();
diff --git a/scene/main/viewport.h b/scene/main/viewport.h
index 03cc39ee92c..0ed3864b08e 100644
--- a/scene/main/viewport.h
+++ b/scene/main/viewport.h
@@ -730,6 +730,7 @@ public:
 
 	Transform2D get_screen_transform() const;
 	virtual Transform2D get_screen_transform_internal(bool p_absolute_position = false) const;
+	virtual Transform2D get_popup_base_transform_native() const { return Transform2D(); }
 	virtual Transform2D get_popup_base_transform() const { return Transform2D(); }
 	virtual Viewport *get_section_root_viewport() const { return nullptr; }
 	virtual bool is_attached_in_viewport() const { return false; }
diff --git a/scene/main/window.cpp b/scene/main/window.cpp
index e3eb4bfa6f0..49811492498 100644
--- a/scene/main/window.cpp
+++ b/scene/main/window.cpp
@@ -3028,6 +3028,20 @@ Transform2D Window::get_screen_transform_internal(bool p_absolute_position) cons
 	return embedder_transform * get_final_transform();
 }
 
+Transform2D Window::get_popup_base_transform_native() const {
+	ERR_READ_THREAD_GUARD_V(Transform2D());
+	if (!DisplayServer::get_singleton()->has_feature(DisplayServer::FEATURE_SUBWINDOWS)) {
+		return Transform2D();
+	}
+	Transform2D popup_base_transform;
+	popup_base_transform.set_origin(get_position());
+	popup_base_transform *= get_final_transform();
+	if (get_embedder()) {
+		return get_embedder()->get_popup_base_transform_native() * popup_base_transform;
+	}
+	return popup_base_transform;
+}
+
 Transform2D Window::get_popup_base_transform() const {
 	ERR_READ_THREAD_GUARD_V(Transform2D());
 	if (is_embedding_subwindows()) {
diff --git a/scene/main/window.h b/scene/main/window.h
index b53a3808558..cd023de18e9 100644
--- a/scene/main/window.h
+++ b/scene/main/window.h
@@ -509,6 +509,7 @@ public:
 	virtual Transform2D get_final_transform() const override;
 	virtual Transform2D get_screen_transform_internal(bool p_absolute_position = false) const override;
 	virtual Transform2D get_popup_base_transform() const override;
+	virtual Transform2D get_popup_base_transform_native() const override;
 	virtual Viewport *get_section_root_viewport() const override;
 	virtual bool is_attached_in_viewport() const override;