diff --git a/scene/debugger/scene_debugger.cpp b/scene/debugger/scene_debugger.cpp
index bab94863fb..51f74ac63b 100644
--- a/scene/debugger/scene_debugger.cpp
+++ b/scene/debugger/scene_debugger.cpp
@@ -2084,6 +2084,10 @@ void RuntimeNodeSelect::_update_selection() {
 			continue;
 		}
 
+		if (!ci->is_inside_tree()) {
+			continue;
+		}
+
 		Transform2D xform;
 		// Cameras (overridden or not) don't affect `CanvasLayer`s.
 		if (root->is_canvas_transform_override_enabled() && !(ci->get_canvas_layer_node() && !ci->get_canvas_layer_node()->is_following_viewport())) {
@@ -2132,6 +2136,10 @@ void RuntimeNodeSelect::_update_selection() {
 			continue;
 		}
 
+		if (!node_3d->is_inside_tree()) {
+			continue;
+		}
+
 		// Fallback.
 		AABB bounds(Vector3(-0.5, -0.5, -0.5), Vector3(1, 1, 1));