diff --git a/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/transforms/TransformIndexer.java b/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/transforms/TransformIndexer.java
index 9294aef87526d..6296bdf1277ff 100644
--- a/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/transforms/TransformIndexer.java
+++ b/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/transforms/TransformIndexer.java
@@ -564,7 +564,10 @@ private void finalizeCheckpoint(ActionListener<Void> listener) {
 
     @Override
     protected void afterFinishOrFailure() {
-        finishIndexerThreadShutdown();
+        finishIndexerThreadShutdown(() -> {
+            auditor.info(transformConfig.getId(), "Transform has stopped.");
+            logger.info("[{}] transform has stopped.", transformConfig.getId());
+        });
     }
 
     @Override
@@ -646,12 +649,6 @@ protected void onFailure(Exception exc) {
         }
     }
 
-    @Override
-    protected void onStop() {
-        auditor.info(transformConfig.getId(), "Transform has stopped.");
-        logger.info("[{}] transform has stopped.", transformConfig.getId());
-    }
-
     @Override
     protected void onAbort() {
         auditor.info(transformConfig.getId(), "Received abort request, stopping transform.");
@@ -1203,7 +1200,7 @@ private void startIndexerThreadShutdown() {
         }
     }
 
-    private void finishIndexerThreadShutdown() {
+    private void finishIndexerThreadShutdown(Runnable next) {
         synchronized (context) {
             indexerThreadShuttingDown = false;
             if (saveStateRequestedDuringIndexerThreadShutdown) {
@@ -1212,7 +1209,9 @@ private void finishIndexerThreadShutdown() {
                 if (context.shouldStopAtCheckpoint() && nextCheckpoint == null) {
                     stop();
                 }
-                doSaveState(getState(), getPosition(), () -> {});
+                doSaveState(getState(), getPosition(), next);
+            } else {
+                next.run();
             }
         }
     }