diff --git a/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/autodetect/output/AutoDetectResultProcessor.java b/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/autodetect/output/AutoDetectResultProcessor.java
index b809cf5cb2b..3c73d6f83de 100644
--- a/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/autodetect/output/AutoDetectResultProcessor.java
+++ b/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/autodetect/output/AutoDetectResultProcessor.java
@@ -33,6 +33,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Objects;
 import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.Semaphore;
 
 /**
  * A runnable class that reads the autodetect process output in the
@@ -61,6 +62,7 @@ public class AutoDetectResultProcessor {
     private final JobResultsPersister persister;
 
     final CountDownLatch completionLatch = new CountDownLatch(1);
+    final Semaphore updateModelSnapshotIdSemaphore = new Semaphore(1);
     private final FlushListener flushListener;
 
     /**
@@ -193,14 +195,28 @@ public class AutoDetectResultProcessor {
     protected void updateModelSnapshotIdOnJob(ModelSnapshot modelSnapshot) {
         JobUpdate update = new JobUpdate.Builder(jobId).setModelSnapshotId(modelSnapshot.getSnapshotId()).build();
         UpdateJobAction.Request updateRequest = new UpdateJobAction.Request(jobId, update);
+
+        try {
+            // This blocks the main processing thread in the unlikely event
+            // there are 2 model snapshots queued up. But it also has the
+            // advantage of ensuring order
+            updateModelSnapshotIdSemaphore.acquire();
+        } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
+            LOGGER.info("[{}] Interrupted acquiring update model snaphot semaphore", jobId);
+            return;
+        }
+
         client.execute(UpdateJobAction.INSTANCE, updateRequest, new ActionListener<PutJobAction.Response>() {
             @Override
             public void onResponse(PutJobAction.Response response) {
+                updateModelSnapshotIdSemaphore.release();
                 LOGGER.debug("[{}] Updated job with model snapshot id [{}]", jobId, modelSnapshot.getSnapshotId());
             }
 
             @Override
             public void onFailure(Exception e) {
+                updateModelSnapshotIdSemaphore.release();
                 LOGGER.error("[" + jobId + "] Failed to update job with new model snapshot id [" + modelSnapshot.getSnapshotId() + "]", e);
             }
         });
@@ -209,8 +225,13 @@ public class AutoDetectResultProcessor {
     public void awaitCompletion() {
         try {
             completionLatch.await();
+            // Input stream has been completely processed at this point.
+            // Wait for any updateModelSnapshotIdOnJob calls to complete.
+            updateModelSnapshotIdSemaphore.acquire();
+            updateModelSnapshotIdSemaphore.release();
         } catch (InterruptedException e) {
             Thread.currentThread().interrupt();
+            LOGGER.info("[{}] Interrupted waiting for results processor to complete", jobId);
         }
     }
 
diff --git a/plugin/src/test/java/org/elasticsearch/xpack/ml/job/process/autodetect/output/AutoDetectResultProcessorTests.java b/plugin/src/test/java/org/elasticsearch/xpack/ml/job/process/autodetect/output/AutoDetectResultProcessorTests.java
index ffb82c2bc35..73b1ac8a672 100644
--- a/plugin/src/test/java/org/elasticsearch/xpack/ml/job/process/autodetect/output/AutoDetectResultProcessorTests.java
+++ b/plugin/src/test/java/org/elasticsearch/xpack/ml/job/process/autodetect/output/AutoDetectResultProcessorTests.java
@@ -291,4 +291,19 @@ public class AutoDetectResultProcessorTests extends ESTestCase {
         verifyNoMoreInteractions(persister);
         verifyNoMoreInteractions(renormalizer);
     }
+
+    public void testAwaitCompletion() {
+        AutodetectResult autodetectResult = mock(AutodetectResult.class);
+        @SuppressWarnings("unchecked")
+        Iterator<AutodetectResult> iterator = mock(Iterator.class);
+        when(iterator.hasNext()).thenReturn(true).thenReturn(false);
+        when(iterator.next()).thenReturn(autodetectResult);
+        AutodetectProcess process = mock(AutodetectProcess.class);
+        when(process.readAutodetectResults()).thenReturn(iterator);
+        processorUnderTest.process(process, randomBoolean());
+
+        processorUnderTest.awaitCompletion();
+        assertEquals(0, processorUnderTest.completionLatch.getCount());
+        assertEquals(1, processorUnderTest.updateModelSnapshotIdSemaphore.availablePermits());
+    }
 }