diff --git a/scene/main/node.cpp b/scene/main/node.cpp
index bec01762d86d..8b5883a742c6 100644
--- a/scene/main/node.cpp
+++ b/scene/main/node.cpp
@@ -229,15 +229,32 @@ void Node::_propagate_enter_tree() {
 }
 
 void Node::_propagate_after_exit_tree() {
+	// Clear owner if it was not part of the pruned branch
 	if (data.owner) {
-		data.owner->data.owned.erase(data.OW);
-		data.owner = nullptr;
+		bool found = false;
+		Node *parent = data.parent;
+
+		while (parent) {
+			if (parent == data.owner) {
+				found = true;
+				break;
+			}
+
+			parent = parent->data.parent;
+		}
+
+		if (!found) {
+			data.owner->data.owned.erase(data.OW);
+			data.owner = nullptr;
+		}
 	}
+
 	data.blocked++;
 	for (int i = data.children.size() - 1; i >= 0; i--) {
 		data.children[i]->_propagate_after_exit_tree();
 	}
 	data.blocked--;
+
 	emit_signal(SceneStringNames::get_singleton()->tree_exited);
 }