diff --git a/editor/doc/editor_help.cpp b/editor/doc/editor_help.cpp
index 3ed2c033d8..ed9a3f453b 100644
--- a/editor/doc/editor_help.cpp
+++ b/editor/doc/editor_help.cpp
@@ -4686,7 +4686,7 @@ void EditorHelpBitTooltip::popup_under_cursor() {
 	// When `FLAG_POPUP` is false, it prevents the editor from losing focus when displaying the tooltip.
 	// This way, clicks and double-clicks are still available outside the tooltip.
 	set_flag(Window::FLAG_POPUP, false);
-	set_flag(Window::FLAG_NO_FOCUS, !is_embedded());
+	set_flag(Window::FLAG_NO_FOCUS, true);
 	popup(r);
 }
 
diff --git a/scene/main/viewport.cpp b/scene/main/viewport.cpp
index f02ab52a9d..1f81119eac 100644
--- a/scene/main/viewport.cpp
+++ b/scene/main/viewport.cpp
@@ -3092,6 +3092,24 @@ bool Viewport::_sub_windows_forward_input(const Ref<InputEvent> &p_event) {
 	}
 
 	if (!gui.subwindow_focused) {
+		// No window focus, check for unfocusable windows under the cursor.
+		Ref<InputEventMouse> me = p_event;
+		if (me.is_valid()) {
+			for (int i = gui.sub_windows.size() - 1; i >= 0; i--) {
+				const SubWindow &sw = gui.sub_windows[i];
+				if (!sw.window->get_flag(Window::FLAG_NO_FOCUS) || sw.window->get_flag(Window::FLAG_MOUSE_PASSTHROUGH)) {
+					continue;
+				}
+				Rect2i r = Rect2i(sw.window->get_position(), sw.window->get_size());
+				if (r.has_point(me->get_position())) {
+					Transform2D window_ofs;
+					window_ofs.set_origin(-sw.window->get_position());
+					Ref<InputEvent> ev = p_event->xformed_by(window_ofs);
+					sw.window->_window_input(ev);
+					return true;
+				}
+			}
+		}
 		return false;
 	}