diff --git a/scene/2d/tile_map.cpp b/scene/2d/tile_map.cpp
index 1836cc20b61..09effe65968 100644
--- a/scene/2d/tile_map.cpp
+++ b/scene/2d/tile_map.cpp
@@ -1839,6 +1839,17 @@ void TileMapLayer::set_cell(const Vector2i &p_coords, int p_source_id, const Vec
 		ERR_FAIL_COND(!Q);
 		TileMapQuadrant &q = Q->value;
 
+		// Find node in scenes and remove it.
+		HashMap<Vector2i, String>::Iterator entry = q.scenes.find(pk);
+		if (entry != q.scenes.end()) {
+			String scene_name = entry->value;
+			Node *scene = tile_map_node->get_node_or_null(scene_name);
+			if (scene) {
+				scene->queue_free();
+				instantiated_scenes.erase(Vector2i(pk.x, pk.y));
+			}
+		}
+
 		q.cells.erase(pk);
 
 		// Remove or make the quadrant dirty.