diff --git a/src/bonsai/bonsai/bim/module/aggregate/operator.py b/src/bonsai/bonsai/bim/module/aggregate/operator.py
index 5fa6885335..e94199b208 100644
--- a/src/bonsai/bonsai/bim/module/aggregate/operator.py
+++ b/src/bonsai/bonsai/bim/module/aggregate/operator.py
@@ -127,6 +127,10 @@ class BIM_OT_aggregate_unassign_object(bpy.types.Operator, tool.Ifc.Operator):
         # Second pass: delete aggregates that now have no parts
         deleted_aggregates = []
         for aggregate in aggregates_to_check:
+            # Skip spatial elements - they should not be deleted even if empty
+            if aggregate.is_a("IfcSpatialElement"):
+                continue
+            
             related_objects = ifcopenshell.util.element.get_parts(aggregate)
             if len(related_objects) == 0:
                 aggregate_name = aggregate.Name or f"{aggregate.is_a()} #{aggregate.id()}"
diff --git a/src/bonsai/bonsai/bim/module/geometry/operator.py b/src/bonsai/bonsai/bim/module/geometry/operator.py
index a27849da31..903473b1b6 100644
--- a/src/bonsai/bonsai/bim/module/geometry/operator.py
+++ b/src/bonsai/bonsai/bim/module/geometry/operator.py
@@ -975,6 +975,10 @@ class OverrideDelete(bpy.types.Operator):
             except:
                 continue
 
+            # Skip spatial elements - they should not be deleted even if empty
+            if aggregate.is_a("IfcSpatialElement"):
+                continue
+
             related_objects = ifcopenshell.util.element.get_parts(aggregate)
             if len(related_objects) == 0:
                 aggregate_name = aggregate.Name or f"{aggregate.is_a()} #{aggregate.id()}"