diff --git a/scene/main/viewport.cpp b/scene/main/viewport.cpp
index 6888283a98e..972f20a50de 100644
--- a/scene/main/viewport.cpp
+++ b/scene/main/viewport.cpp
@@ -272,17 +272,31 @@ void Viewport::_sub_window_update_order() {
 		return;
 	}
 
-	if (!gui.sub_windows[gui.sub_windows.size() - 1].window->get_flag(Window::FLAG_ALWAYS_ON_TOP)) {
-		int index = gui.sub_windows.size() - 1;
-
-		while (index > 0 && gui.sub_windows[index - 1].window->get_flag(Window::FLAG_ALWAYS_ON_TOP)) {
-			--index;
+	// Reorder 'always on top' windows.
+	int last_index = gui.sub_windows.size() - 1;
+	for (int index = last_index, insert_index = last_index; index >= 0; index--) {
+		SubWindow sw = gui.sub_windows[index];
+		Window *parent_window = sw.window->get_parent_visible_window();
+		bool parent_is_always_on_top = (parent_window != nullptr) && parent_window->get_flag(Window::FLAG_ALWAYS_ON_TOP);
+		if (sw.window->get_flag(Window::FLAG_ALWAYS_ON_TOP) || (parent_is_always_on_top && sw.window->is_exclusive())) {
+			if (index != insert_index) {
+				gui.sub_windows.remove_at(index);
+				gui.sub_windows.insert(insert_index, sw);
+			}
+			insert_index--;
 		}
+	}
 
-		if (index != (gui.sub_windows.size() - 1)) {
-			SubWindow sw = gui.sub_windows[gui.sub_windows.size() - 1];
-			gui.sub_windows.remove_at(gui.sub_windows.size() - 1);
-			gui.sub_windows.insert(index, sw);
+	// Reorder exclusive children.
+	for (int parent_index = 0; parent_index < gui.sub_windows.size(); parent_index++) {
+		Window *exclusive_child = gui.sub_windows[parent_index].window->get_exclusive_child();
+		if (exclusive_child != nullptr && exclusive_child->is_visible()) {
+			int child_index = _sub_window_find(exclusive_child);
+			if (child_index < parent_index) {
+				SubWindow sw = gui.sub_windows[child_index];
+				gui.sub_windows.remove_at(child_index);
+				gui.sub_windows.insert(parent_index, sw);
+			}
 		}
 	}