diff --git a/scene/main/viewport.cpp b/scene/main/viewport.cpp
index dd3ae1ad3cb..373af20d352 100644
--- a/scene/main/viewport.cpp
+++ b/scene/main/viewport.cpp
@@ -682,8 +682,9 @@ void Viewport::_process_picking() {
 	if (Object::cast_to<Window>(this) && Input::get_singleton()->get_mouse_mode() == Input::MOUSE_MODE_CAPTURED) {
 		return;
 	}
-	if (!gui.mouse_in_viewport) {
-		// Clear picking events if mouse has left viewport.
+	if (!gui.mouse_in_viewport || gui.subwindow_over) {
+		// Clear picking events if the mouse has left the viewport or is over an embedded window.
+		// These are locations, that are expected to not trigger physics picking.
 		physics_picking_events.clear();
 		return;
 	}