diff --git a/src/state.rs b/src/state.rs
index 487d50f9..ae366f72 100644
--- a/src/state.rs
+++ b/src/state.rs
@@ -1006,6 +1006,7 @@ impl State {
         self.run_toplevel.clear();
         self.xwayland.handler.borrow_mut().take();
         self.xwayland.queue.clear();
+        self.xwayland.windows.clear();
         self.idle.inhibitors.clear();
         self.idle.change.clear();
         for drm_dev in self.drm_devs.lock().drain_values() {
diff --git a/src/xwayland.rs b/src/xwayland.rs
index 6d6fb1e1..b5a65f48 100644
--- a/src/xwayland.rs
+++ b/src/xwayland.rs
@@ -203,6 +203,7 @@ async fn run(
         state.ring.readable(&pidfd).await?;
     }
     state.xwayland.queue.clear();
+    state.xwayland.windows.clear();
     stderr_read.await;
     Ok(())
 }