diff --git a/openpype/hosts/nuke/api/pipeline.py b/openpype/hosts/nuke/api/pipeline.py
index 58cd445388..e739d7335e 100644
--- a/openpype/hosts/nuke/api/pipeline.py
+++ b/openpype/hosts/nuke/api/pipeline.py
@@ -545,7 +545,8 @@ def remove_instance(instance):
         instance (dict): instance representation from subsetmanager model
     """
     instance_node = instance.transient_data["node"]
-    nuke.delete(instance_node)
+    instance_knob = instance_node.knobs()[INSTANCE_DATA_KNOB]
+    instance_node.removeKnob(instance_knob)
 
 
 def select_instance(instance):