diff --git a/scene/main/viewport.cpp b/scene/main/viewport.cpp
index 9c8385374dc..233f50e7c4e 100644
--- a/scene/main/viewport.cpp
+++ b/scene/main/viewport.cpp
@@ -3217,7 +3217,7 @@ void Viewport::_window_start_resize(SubWindowResize p_edge, Window *p_window) {
 	_sub_window_update(sw.window);
 }
 
-void Viewport::_update_mouse_over() {
+void Viewport::_update_mouse_over(const Ref<InputEventMouse> &p_mm) {
 	// Update gui.mouse_over and gui.subwindow_over in all Viewports.
 	// Send necessary mouse_enter/mouse_exit signals and the MOUSE_ENTER/MOUSE_EXIT notifications for every Viewport in the SceneTree.
 
@@ -3228,18 +3228,20 @@ void Viewport::_update_mouse_over() {
 
 	if (get_tree()->get_root()->is_embedding_subwindows() || is_sub_viewport()) {
 		// Use embedder logic for calculating mouse position.
-		_update_mouse_over(gui.last_mouse_pos);
+		_update_mouse_over(p_mm->get_position());
 	} else {
 		// Native Window: Use DisplayServer logic for calculating mouse position.
 		Window *receiving_window = get_tree()->get_root()->gui.windowmanager_window_over;
 		if (!receiving_window) {
 			return;
 		}
-
-		Vector2 pos = DisplayServer::get_singleton()->mouse_get_position() - receiving_window->get_position();
-		pos = receiving_window->get_final_transform().affine_inverse().xform(pos);
-
-		receiving_window->_update_mouse_over(pos);
+		if (receiving_window->get_window_id() != p_mm->get_window_id()) {
+			Vector2 pos = DisplayServer::get_singleton()->mouse_get_position() - receiving_window->get_position();
+			pos = receiving_window->get_final_transform().affine_inverse().xform(pos);
+			receiving_window->_update_mouse_over(pos);
+		} else {
+			receiving_window->_update_mouse_over(p_mm->get_position());
+		}
 	}
 }
 
@@ -3487,9 +3489,7 @@ void Viewport::push_input(RequiredParam<InputEvent> rp_event, bool p_local_coord
 
 	Ref<InputEventMouse> me = ev;
 	if (me.is_valid()) {
-		gui.last_mouse_pos = me->get_position();
-
-		_update_mouse_over();
+		_update_mouse_over(me);
 	}
 
 	if (is_embedding_subwindows() && _sub_windows_forward_input(ev)) {
diff --git a/scene/main/viewport.h b/scene/main/viewport.h
index bf512813b10..f45cc337532 100644
--- a/scene/main/viewport.h
+++ b/scene/main/viewport.h
@@ -488,7 +488,7 @@ private:
 	bool _sub_windows_forward_input(const Ref<InputEvent> &p_event);
 	SubWindowResize _sub_window_get_resize_margin(Window *p_subwindow, const Point2 &p_point);
 
-	void _update_mouse_over();
+	void _update_mouse_over(const Ref<InputEventMouse> &p_mm);
 	virtual void _update_mouse_over(Vector2 p_pos);
 	virtual void _mouse_leave_viewport();