diff --git a/community/kernel/src/main/java/org/neo4j/kernel/impl/api/CountsStoreTransactionApplier.java b/community/kernel/src/main/java/org/neo4j/kernel/impl/api/CountsStoreTransactionApplier.java
index da307c297b12..b95c4636b750 100644
--- a/community/kernel/src/main/java/org/neo4j/kernel/impl/api/CountsStoreTransactionApplier.java
+++ b/community/kernel/src/main/java/org/neo4j/kernel/impl/api/CountsStoreTransactionApplier.java
@@ -23,6 +23,7 @@
 
 import org.neo4j.kernel.impl.store.counts.CountsTracker;
 import org.neo4j.kernel.impl.transaction.command.Command;
+import org.neo4j.kernel.impl.transaction.command.Command.SchemaRuleCommand;
 import org.neo4j.storageengine.api.TransactionApplicationMode;
 
 public class CountsStoreTransactionApplier extends TransactionApplier.Adapter
@@ -40,6 +41,11 @@ public CountsStoreTransactionApplier( TransactionApplicationMode mode, CountsAcc
     public void close() throws Exception
     {
         assert countsUpdater != null || mode == TransactionApplicationMode.RECOVERY : "You must call begin first";
+        closeCountsUpdaterIfOpen();
+    }
+
+    private void closeCountsUpdaterIfOpen()
+    {
         if ( countsUpdater != null )
         {   // CountsUpdater is null if we're in recovery and the counts store already has had this transaction applied.
             countsUpdater.close();
@@ -68,4 +74,15 @@ public boolean visitRelationshipCountsCommand( Command.RelationshipCountsCommand
         }
         return false;
     }
+
+    @Override
+    public boolean visitSchemaRuleCommand( SchemaRuleCommand command ) throws IOException
+    {
+        // This shows that this transaction is a schema transaction, so it cannot have commands
+        // updating any counts anyway. Therefore the counts updater is closed right away.
+        // This also breaks an otherwise deadlocking scenario between check pointer, this applier
+        // and an index population thread wanting to apply index sampling to the counts store.
+        closeCountsUpdaterIfOpen();
+        return false;
+    }
 }
diff --git a/community/kernel/src/main/java/org/neo4j/kernel/impl/storageengine/impl/recordstorage/RecordStorageEngine.java b/community/kernel/src/main/java/org/neo4j/kernel/impl/storageengine/impl/recordstorage/RecordStorageEngine.java
index b230a5db5d83..d8a2410c95a1 100644
--- a/community/kernel/src/main/java/org/neo4j/kernel/impl/storageengine/impl/recordstorage/RecordStorageEngine.java
+++ b/community/kernel/src/main/java/org/neo4j/kernel/impl/storageengine/impl/recordstorage/RecordStorageEngine.java
@@ -374,6 +374,9 @@ protected BatchTransactionApplierFacade applier( TransactionApplicationMode mode
             appliers.add( new CacheInvalidationBatchTransactionApplier( neoStores, cacheAccess ) );
         }
 
+        // Counts store application
+        appliers.add( new CountsStoreBatchTransactionApplier( neoStores.getCounts(), mode ) );
+
         // Schema index application
         appliers.add( new IndexBatchTransactionApplier( indexingService, labelScanStoreSync, indexUpdatesSync,
                 neoStores.getNodeStore(), new PropertyLoader( neoStores ),
@@ -384,9 +387,6 @@ protected BatchTransactionApplierFacade applier( TransactionApplicationMode mode
                 new LegacyBatchIndexApplier( indexConfigStore, legacyIndexApplierLookup, legacyIndexTransactionOrdering,
                         mode ) );
 
-        // Counts store application
-        appliers.add( new CountsStoreBatchTransactionApplier( neoStores.getCounts(), mode ) );
-
         // Perform the application
         return new BatchTransactionApplierFacade(
                 appliers.toArray( new BatchTransactionApplier[appliers.size()] ) );
diff --git a/community/kernel/src/test/java/org/neo4j/kernel/impl/transaction/log/checkpoint/CheckPointerConstraintCreationDeadlockIT.java b/community/kernel/src/test/java/org/neo4j/kernel/impl/transaction/log/checkpoint/CheckPointerConstraintCreationDeadlockIT.java
index afc886a79e97..be22acb62c09 100644
--- a/community/kernel/src/test/java/org/neo4j/kernel/impl/transaction/log/checkpoint/CheckPointerConstraintCreationDeadlockIT.java
+++ b/community/kernel/src/test/java/org/neo4j/kernel/impl/transaction/log/checkpoint/CheckPointerConstraintCreationDeadlockIT.java
@@ -117,7 +117,15 @@ public void indexPopulationScanComplete()
             Future<Object> checkPointer = t3.execute( state ->
                     db.getDependencyResolver().resolveDependency( CheckPointer.class )
                             .forceCheckPoint( new SimpleTriggerInfo( "MANUAL" ) ) );
-            t3.get().waitUntilWaiting( details -> details.isAt( LockWrapper.class, "writeLock" ) );
+            try
+            {
+                t3.get().waitUntilWaiting( details -> details.isAt( LockWrapper.class, "writeLock" ) );
+            }
+            catch ( IllegalStateException e )
+            {
+                // Thrown when the fix is in, basically it's thrown if the check pointer didn't get blocked
+                checkPointer.get(); // to assert that no exception was thrown during in check point thread
+            }
 
             // Alright the trap is set. Let the population thread move on and seal the deal
             controller.release();