diff --git a/include/sway/layers.h b/include/sway/layers.h
index a7afb9001..fd6384e0e 100644
--- a/include/sway/layers.h
+++ b/include/sway/layers.h
@@ -3,6 +3,7 @@
 #include <stdbool.h>
 #include <wlr/types/wlr_compositor.h>
 #include <wlr/types/wlr_layer_shell_v1.h>
+#include "sway/tree/view.h"
 
 struct sway_layer_surface {
 	struct wl_listener map;
@@ -14,10 +15,12 @@ struct sway_layer_surface {
 
 	bool mapped;
 
+	struct wlr_scene_tree *popups;
+	struct sway_popup_desc desc;
+
 	struct sway_output *output;
 	struct wlr_scene_layer_surface_v1 *scene;
 	struct wlr_scene_tree *tree;
-	struct wlr_scene_tree *popups;
 	struct wlr_layer_surface_v1 *layer_surface;
 };
 
diff --git a/sway/desktop/layer_shell.c b/sway/desktop/layer_shell.c
index 9a35ef95a..769d3a865 100644
--- a/sway/desktop/layer_shell.c
+++ b/sway/desktop/layer_shell.c
@@ -122,6 +122,16 @@ static struct sway_layer_surface *sway_layer_surface_create(
 		return NULL;
 	}
 
+	surface->desc.relative = &scene->tree->node;
+
+	if (!scene_descriptor_assign(&popups->node,
+			SWAY_SCENE_DESC_POPUP, &surface->desc)) {
+		sway_log(SWAY_ERROR, "Failed to allocate a popup scene descriptor");
+		wlr_scene_node_destroy(&popups->node);
+		free(surface);
+		return NULL;
+	}
+
 	surface->tree = scene->tree;
 	surface->scene = scene;
 	surface->layer_surface = scene->layer_surface;
@@ -224,10 +234,6 @@ static void handle_surface_commit(struct wl_listener *listener, void *data) {
 		arrange_layers(surface->output);
 		transaction_commit_dirty();
 	}
-
-	int lx, ly;
-	wlr_scene_node_coords(&surface->scene->tree->node, &lx, &ly);
-	wlr_scene_node_set_position(&surface->popups->node, lx, ly);
 }
 
 static void handle_map(struct wl_listener *listener, void *data) {
diff --git a/sway/desktop/transaction.c b/sway/desktop/transaction.c
index e3196e3af..fd1c3d3a1 100644
--- a/sway/desktop/transaction.c
+++ b/sway/desktop/transaction.c
@@ -612,13 +612,9 @@ void arrange_popups(struct wlr_scene_tree *popups) {
 		struct sway_popup_desc *popup = scene_descriptor_try_get(node,
 			SWAY_SCENE_DESC_POPUP);
 
-		// the popup layer may have popups from layer_shell surfaces, in this
-		// case those don't have a scene descriptor, so lets skip those here.
-		if (popup) {
-			int lx, ly;
-			wlr_scene_node_coords(popup->relative, &lx, &ly);
-			wlr_scene_node_set_position(node, lx, ly);
-		}
+		int lx, ly;
+		wlr_scene_node_coords(popup->relative, &lx, &ly);
+		wlr_scene_node_set_position(node, lx, ly);
 	}
 }
 
diff --git a/sway/input/cursor.c b/sway/input/cursor.c
index f25439cbc..25fa603ef 100644
--- a/sway/input/cursor.c
+++ b/sway/input/cursor.c
@@ -92,7 +92,7 @@ struct sway_node *node_at_coords(
 			if (!con) {
 				struct sway_popup_desc *popup =
 					scene_descriptor_try_get(current, SWAY_SCENE_DESC_POPUP);
-				if (popup) {
+				if (popup && popup->view) {
 					con = popup->view->container;
 				}
 			}