diff --git a/Editor/PluginDefinition/PluginDefinition.cs b/Editor/PluginDefinition/PluginDefinition.cs
index b73e5a32..742a1e17 100644
--- a/Editor/PluginDefinition/PluginDefinition.cs
+++ b/Editor/PluginDefinition/PluginDefinition.cs
@@ -7,6 +7,7 @@ using nadena.dev.modular_avatar.editor.ErrorReporting;
 using nadena.dev.ndmf;
 using nadena.dev.ndmf.animator;
 using nadena.dev.ndmf.fluent;
+using nadena.dev.ndmf.util;
 using UnityEngine;
 using Object = UnityEngine.Object;
 
@@ -76,6 +77,8 @@ namespace nadena.dev.modular_avatar.core.editor.plugin
 #endif
                     seq.Run(MergeArmaturePluginPass.Instance);
 
+                    seq.Run("Prune empty animator layers",
+                        ctx => { ctx.Extension<AnimatorServicesContext>().RemoveEmptyLayers(); });
                 });
                 
                 seq.WithRequiredExtension(typeof(AnimationServicesContext), _s2 =>
diff --git a/UnitTests~/Animation/LayerPruningTest.cs b/UnitTests~/Animation/LayerPruningTest.cs
index c5af1638..40cd179c 100644
--- a/UnitTests~/Animation/LayerPruningTest.cs
+++ b/UnitTests~/Animation/LayerPruningTest.cs
@@ -32,8 +32,12 @@ namespace modular_avatar_tests
             Assert.AreEqual("L3", l3.name);
             Assert.AreEqual("L3.a", l3a.name);
 
-            Assert.AreEqual(2, l3.stateMachine.defaultState.behaviours.Length);
-            Assert.AreEqual(4, ((VRCAnimatorLayerControl)l3.stateMachine.defaultState.behaviours[0]).layer);
+            // The layer control behavior referencing the deleted layer should be removed
+            Assert.AreEqual(3, l3.stateMachine.defaultState.behaviours.Length);
+            Assert.AreEqual("2", ((VRCAnimatorLayerControl)l3.stateMachine.defaultState.behaviours[0]).debugString);
+            Assert.IsTrue(l3.stateMachine.defaultState.behaviours[1] is VRCAnimatorTrackingControl);
+            Assert.AreEqual("3", ((VRCAnimatorLayerControl)l3.stateMachine.defaultState.behaviours[2]).debugString);
+            Assert.AreEqual(3, ((VRCAnimatorLayerControl)l3.stateMachine.defaultState.behaviours[0]).layer);
             
             Assert.AreEqual(1, l3a.stateMachine.defaultState.behaviours.Length);
             Assert.AreEqual(3, ((VRCAnimatorLayerControl)l3a.stateMachine.defaultState.behaviours[0]).layer);
diff --git a/UnitTests~/Animation/LayerPruningTest/AC3.controller b/UnitTests~/Animation/LayerPruningTest/AC3.controller
index 4df78521..0f9264ba 100644
--- a/UnitTests~/Animation/LayerPruningTest/AC3.controller
+++ b/UnitTests~/Animation/LayerPruningTest/AC3.controller
@@ -1,5 +1,22 @@
 %YAML 1.1
 %TAG !u! tag:unity3d.com,2011:
+--- !u!114 &-8943217745761122886
+MonoBehaviour:
+  m_ObjectHideFlags: 1
+  m_CorrespondingSourceObject: {fileID: 0}
+  m_PrefabInstance: {fileID: 0}
+  m_PrefabAsset: {fileID: 0}
+  m_GameObject: {fileID: 0}
+  m_Enabled: 1
+  m_EditorHideFlags: 0
+  m_Script: {fileID: -1936262289, guid: 67cc4cb7839cd3741b63733d5adf0442, type: 3}
+  m_Name: 
+  m_EditorClassIdentifier: 
+  playable: 0
+  layer: 0
+  goalWeight: 0
+  blendDuration: 0
+  debugString: 3
 --- !u!1107 &-6599268793956612610
 AnimatorStateMachine:
   serializedVersion: 6
@@ -76,6 +93,7 @@ AnimatorState:
   - {fileID: 2645212092703721488}
   - {fileID: -4263003778027536188}
   - {fileID: 1637143755065747004}
+  - {fileID: -8943217745761122886}
   m_Position: {x: 50, y: 50, z: 0}
   m_IKOnFeet: 0
   m_WriteDefaultValues: 1
@@ -102,8 +120,8 @@ MonoBehaviour:
   m_Script: {fileID: -1936262289, guid: 67cc4cb7839cd3741b63733d5adf0442, type: 3}
   m_Name: 
   m_EditorClassIdentifier: 
-  playable: 0
-  layer: 0
+  playable: 1
+  layer: 1
   goalWeight: 0
   blendDuration: 0
   debugString: 2