--- a/src/view/xdg-shell.cpp
+++ b/src/view/xdg-shell.cpp
@@ -15,6 +15,7 @@
 #include "xdg-shell.hpp"
 #include "wayfire/output-layout.hpp"
 #include <wayfire/workspace-set.hpp>
+#include <wayfire/window-scope.hpp>
 #include <wayfire/signal-definitions.hpp>
 #include <wayfire/unstable/wlr-surface-controller.hpp>
 #include <wayfire/unstable/wlr-view-events.hpp>
@@ -313,6 +314,14 @@
     }
 
     auto box = get_output()->get_relative_geometry();
+    if (auto toplevel = wf::toplevel_cast(toplevel_parent))
+    {
+        // Popup positioners use the toplevel's coordinate system. Keep a
+        // physical-scope application's menus on its member of a stitched
+        // output, while virtual-scope and layer-shell parents retain the
+        // logical output bounds.
+        box = wf::window_scope_fullscreen(toplevel);
+    }
     auto parent_offset = toplevel_parent->get_surface_root_node()->to_global({0, 0});
     box.x -= parent_offset.x;
     box.y -= parent_offset.y;