diff --git a/platform/linuxbsd/wayland/display_server_wayland.cpp b/platform/linuxbsd/wayland/display_server_wayland.cpp
index 60a4f4d1f83..421c16f67ae 100644
--- a/platform/linuxbsd/wayland/display_server_wayland.cpp
+++ b/platform/linuxbsd/wayland/display_server_wayland.cpp
@@ -1236,12 +1236,12 @@ void DisplayServerWayland::window_set_flag(WindowFlags p_flag, bool p_enabled, D
 
 		case WINDOW_FLAG_POPUP: {
 			ERR_FAIL_COND_MSG(p_window_id == MAIN_WINDOW_ID, "Main window can't be popup.");
-			ERR_FAIL_COND_MSG(wd.visible, "Popup flag can't changed while window is opened.");
+			ERR_FAIL_COND_MSG(wd.visible && (wd.flags & WINDOW_FLAG_POPUP_BIT) != p_enabled, "Popup flag can't changed while window is opened.");
 		} break;
 
 		case WINDOW_FLAG_POPUP_WM_HINT: {
 			ERR_FAIL_COND_MSG(p_window_id == MAIN_WINDOW_ID, "Main window can't have popup hint.");
-			ERR_FAIL_COND_MSG(wd.visible, "Popup hint can't changed while window is opened.");
+			ERR_FAIL_COND_MSG(wd.visible && (wd.flags & WINDOW_FLAG_POPUP_WM_HINT_BIT) != p_enabled, "Popup hint can't changed while window is opened.");
 		} break;
 
 		default: {