diff --git a/pulsar-broker/src/main/java/org/apache/pulsar/broker/loadbalance/extensions/channel/ServiceUnitStateChannelImpl.java b/pulsar-broker/src/main/java/org/apache/pulsar/broker/loadbalance/extensions/channel/ServiceUnitStateChannelImpl.java
index f3a308add9ef1d..6246c26e57bccc 100644
--- a/pulsar-broker/src/main/java/org/apache/pulsar/broker/loadbalance/extensions/channel/ServiceUnitStateChannelImpl.java
+++ b/pulsar-broker/src/main/java/org/apache/pulsar/broker/loadbalance/extensions/channel/ServiceUnitStateChannelImpl.java
@@ -1152,9 +1152,9 @@ private void overrideOwnership(String serviceUnit, ServiceUnitStateData orphanDa
         }
     }
 
-    protected void waitForCleanups(boolean excludeSystemTopics, int timeoutInMillis) {
+    private void waitForCleanups(String broker, boolean excludeSystemTopics, int maxWaitTimeInMillis) {
         long started = System.currentTimeMillis();
-        while (System.currentTimeMillis() - started < timeoutInMillis) {
+        while (System.currentTimeMillis() - started < maxWaitTimeInMillis) {
             boolean cleaned = true;
             for (var etr : tableview.entrySet()) {
                 var serviceUnit = etr.getKey();
@@ -1164,7 +1164,7 @@ protected void waitForCleanups(boolean excludeSystemTopics, int timeoutInMillis)
                     continue;
                 }
 
-                if (data.state() == Owned && data.dstBroker().equals(lookupServiceAddress)) {
+                if (data.state() == Owned && broker.equals(data.dstBroker())) {
                     cleaned = false;
                     break;
                 }
@@ -1228,7 +1228,12 @@ private synchronized void doCleanup(String broker)  {
 
 
         if (orphanServiceUnitCleanupCnt > 0) {
-            waitForCleanups(true, OWNERSHIP_CLEAN_UP_MAX_WAIT_TIME_IN_MILLIS);
+            // System bundles can contain this channel's system topic and other important system topics.
+            // Cleaning such system bundles(closing the system topics) together with the non-system bundles
+            // can cause the cluster to be temporarily unstable.
+            // Hence, we clean the non-system bundles first and gracefully wait for them.
+            // After that, we clean the system bundles, if any.
+            waitForCleanups(broker, true, OWNERSHIP_CLEAN_UP_MAX_WAIT_TIME_IN_MILLIS);
             this.totalOrphanServiceUnitCleanupCnt += orphanServiceUnitCleanupCnt;
             this.totalInactiveBrokerCleanupCnt++;
         }