diff --git a/helix-core/src/main/java/org/apache/helix/controller/stages/IntermediateStateCalcStage.java b/helix-core/src/main/java/org/apache/helix/controller/stages/IntermediateStateCalcStage.java
index ec17b620c9b..477e4f99bf6 100644
--- a/helix-core/src/main/java/org/apache/helix/controller/stages/IntermediateStateCalcStage.java
+++ b/helix-core/src/main/java/org/apache/helix/controller/stages/IntermediateStateCalcStage.java
@@ -367,11 +367,11 @@ private PartitionStateMap computeIntermediatePartitionState(ResourceControllerDa
           currentStateOutput.getCurrentStateMap(resourceName, partition).entrySet().stream()
               .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue));
       List<String> preferenceList = preferenceLists.get(partition.getPartitionName());
-      if (preferenceList == null || preferenceList.size() == 0) {
-        continue;
-      }
       Map<String, Integer> requiredState = getRequiredStates(resourceName, cache, preferenceList);
-      messagesToThrottle.sort(new MessagePriorityComparator(preferenceList, stateModelDef.getStatePriorityMap()));
+      if (preferenceList != null && !preferenceList.isEmpty()) {
+        // Sort messages based on the priority (priority is defined in the state model definition
+        messagesToThrottle.sort(new MessagePriorityComparator(preferenceList, stateModelDef.getStatePriorityMap()));
+      }
       for (Message message : messagesToThrottle) {
         RebalanceType rebalanceType =
             getRebalanceTypePerMessage(requiredState, message, derivedCurrentStateMap);
@@ -470,10 +470,6 @@ private void chargePendingTransition(Resource resource, CurrentStateOutput curre
       // To clarify that custom mode does not apply recovery/load rebalance since user can define different number of
       // replicas for different partitions. Actually, the custom will stopped from resource level checks if this resource
       // is not FULL_AUTO, we will return best possible state and do nothing.
-      List<String> preferenceList = preferenceLists.get(partition.getPartitionName());
-      if (preferenceList == null) {
-        continue;
-      }
       Map<String, Integer> requiredStates =
           getRequiredStates(resourceName, cache, preferenceLists.get(partition.getPartitionName()));
       // Maps instance to its current state
@@ -482,8 +478,11 @@ private void chargePendingTransition(Resource resource, CurrentStateOutput curre
       // Maps instance to its pending (next) state
       List<Message> pendingMessages = new ArrayList<>(
           currentStateOutput.getPendingMessageMap(resourceName, partition).values());
-      pendingMessages.sort(new MessagePriorityComparator(preferenceLists.get(partition.getPartitionName()),
-          stateModelDefinition.getStatePriorityMap()));
+      List<String> preferenceList = preferenceLists.get(partition.getPartitionName());
+      if (preferenceList != null && !preferenceList.isEmpty()) {
+        pendingMessages.sort(new MessagePriorityComparator(preferenceList,
+            stateModelDefinition.getStatePriorityMap()));
+      }
 
       for (Message message : pendingMessages) {
         StateTransitionThrottleConfig.RebalanceType rebalanceType =