diff --git a/SuperTiled2Unity/Assets/SuperTiled2Unity/Scripts/Editor/Importers/TiledAssetImporter.cs b/SuperTiled2Unity/Assets/SuperTiled2Unity/Scripts/Editor/Importers/TiledAssetImporter.cs
index 9253f2a9..2c45a831 100644
--- a/SuperTiled2Unity/Assets/SuperTiled2Unity/Scripts/Editor/Importers/TiledAssetImporter.cs
+++ b/SuperTiled2Unity/Assets/SuperTiled2Unity/Scripts/Editor/Importers/TiledAssetImporter.cs
@@ -61,7 +61,7 @@ public void AddSuperCustomProperties(GameObject go, XElement xProperties, SuperT
             component.m_Properties = properties.OrderBy(p => p.m_Name).ToList();
 
             AssignUnityTag(component);
-            AssignUnityLayer(component);
+            AssignUnityLayer(component, defaultInheritFromParent: true);
         }
 
         public void AssignTilemapSorting(TilemapRenderer renderer)
@@ -146,7 +146,7 @@ protected void AssignUnityTag(SuperCustomProperties properties)
             }
         }
 
-        protected void AssignUnityLayer(SuperCustomProperties properties)
+        protected void AssignUnityLayer(SuperCustomProperties properties, bool defaultInheritFromParent)
         {
             // Do we have a 'unity:layer' property?
             CustomProperty prop;
@@ -163,7 +163,7 @@ protected void AssignUnityLayer(SuperCustomProperties properties)
                     properties.gameObject.layer = LayerMask.NameToLayer(layer);
                 }
             }
-            else
+            else if (defaultInheritFromParent)
             {
                 // Inherit the layer of our parent
                 var parent = properties.gameObject.transform.parent;
diff --git a/SuperTiled2Unity/Assets/SuperTiled2Unity/Scripts/Editor/Importers/TmxAssetImporter.cs b/SuperTiled2Unity/Assets/SuperTiled2Unity/Scripts/Editor/Importers/TmxAssetImporter.cs
index 0abc240f..2c4362b4 100644
--- a/SuperTiled2Unity/Assets/SuperTiled2Unity/Scripts/Editor/Importers/TmxAssetImporter.cs
+++ b/SuperTiled2Unity/Assets/SuperTiled2Unity/Scripts/Editor/Importers/TmxAssetImporter.cs
@@ -412,6 +412,17 @@ private void DoPrefabReplacements()
                     // Keep the name from Tiled.
                     instance.name = so.gameObject.name;
 
+                    // Transfer and reapply custom property magic on the instantiated prefab.
+                    var soComponent = so.gameObject.GetComponent<SuperCustomProperties>();
+                    if (soComponent != null && !soComponent.m_Properties.IsEmpty())
+                    {
+                        var component = instance.AddComponent<SuperCustomProperties>();
+                        component.m_Properties = new List<CustomProperty>();
+                        component.m_Properties.CombineFromSource(soComponent.m_Properties);
+                        AssignUnityTag(component);
+                        AssignUnityLayer(component, defaultInheritFromParent: false);
+                    }
+
                     // Update bookkeeping for later custom property replacement.
                     goToDestroy.Add(so.gameObject);
                     objectsById[so.m_Id] = instance;