diff --git a/Gems/EMotionFX/Code/EMotionFX/Tools/EMotionStudio/Plugins/StandardPlugins/Source/MotionSetsWindow/MotionSetWindow.cpp b/Gems/EMotionFX/Code/EMotionFX/Tools/EMotionStudio/Plugins/StandardPlugins/Source/MotionSetsWindow/MotionSetWindow.cpp
index 393e26790b..3a4c2628b3 100644
--- a/Gems/EMotionFX/Code/EMotionFX/Tools/EMotionStudio/Plugins/StandardPlugins/Source/MotionSetsWindow/MotionSetWindow.cpp
+++ b/Gems/EMotionFX/Code/EMotionFX/Tools/EMotionStudio/Plugins/StandardPlugins/Source/MotionSetsWindow/MotionSetWindow.cpp
@@ -1138,6 +1138,12 @@ namespace EMStudio
             for (size_t motionSetId = 0; motionSetId < numMotionSets; motionSetId++)
             {
                 EMotionFX::MotionSet* motionSet2 = EMotionFX::GetMotionManager().GetMotionSet(motionSetId);
+
+                if (motionSet2->GetIsOwnedByRuntime())
+                {
+                    continue;
+                }
+
                 if (motionSet2->FindMotionEntryById(motionEntry->GetId()))
                 {
                     numMotionSetContainsMotion++;
@@ -1148,12 +1154,6 @@ namespace EMStudio
                 }
             }
 
-            // If motion exists in multiple motion sets, then it should not be removed from motions window.
-            if (removeMotion && numMotionSetContainsMotion > 1)
-            {
-                continue;
-            }
-
             // check the reference counter if only one reference registered
             // two is needed because the remove motion command has to be called to have the undo/redo possible
             // without it the motion list is also not updated because the remove motion callback is not called
@@ -1170,6 +1170,12 @@ namespace EMStudio
             }
             motionIdsToRemoveString += motionEntry->GetId();
 
+            // If motion exists in multiple motion sets, then it should not be removed from motions window.
+            if (removeMotion && numMotionSetContainsMotion > 1)
+            {
+                continue;
+            }
+
             // Check if the motion is not valid, that means the motion is not loaded.
             if (removeMotion && motionEntry->GetMotion())
             {