diff --git a/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/autodetect/NativeAutodetectProcess.java b/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/autodetect/NativeAutodetectProcess.java
index ec3b0b927dd..b2de0836223 100644
--- a/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/autodetect/NativeAutodetectProcess.java
+++ b/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/autodetect/NativeAutodetectProcess.java
@@ -47,6 +47,8 @@ import java.util.concurrent.TimeoutException;
 class NativeAutodetectProcess implements AutodetectProcess {
     private static final Logger LOGGER = Loggers.getLogger(NativeAutodetectProcess.class);
 
+    private static final Duration WAIT_FOR_KILL_TIMEOUT = Duration.ofMillis(1000);
+
     private final String jobId;
     private final CppLogMessageHandler cppLogHandler;
     private final OutputStream processInStream;
@@ -207,6 +209,10 @@ class NativeAutodetectProcess implements AutodetectProcess {
             // but if the wait times out it implies the process has only just started, in which
             // case it should die very quickly when we close its input stream.
             NativeControllerHolder.getNativeController().killProcess(cppLogHandler.getPid(Duration.ZERO));
+
+            // Wait for the process to die before closing processInStream as if the process
+            // is still alive when processInStream is closed autodetect will start persisting state
+            cppLogHandler.waitForLogStreamClose(WAIT_FOR_KILL_TIMEOUT);
         } catch (TimeoutException e) {
             LOGGER.warn("[{}] Failed to get PID of autodetect process to kill", jobId);
         } finally {
diff --git a/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/logging/CppLogMessageHandler.java b/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/logging/CppLogMessageHandler.java
index c43bb1afbfa..f6df58f385c 100644
--- a/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/logging/CppLogMessageHandler.java
+++ b/plugin/src/main/java/org/elasticsearch/xpack/ml/job/process/logging/CppLogMessageHandler.java
@@ -51,8 +51,8 @@ public class CppLogMessageHandler implements Closeable {
     private final Deque<String> errorStore;
     private final CountDownLatch pidLatch;
     private final CountDownLatch cppCopyrightLatch;
+    private final CountDownLatch logStreamClosedLatch;
     private MessageSummary lastMessageSummary = new MessageSummary();
-    private volatile boolean hasLogStreamEnded;
     private volatile boolean seenFatalError;
     private volatile long pid;
     private volatile String cppCopyright;
@@ -76,7 +76,7 @@ public class CppLogMessageHandler implements Closeable {
         errorStore = ConcurrentCollections.newDeque();
         pidLatch = new CountDownLatch(1);
         cppCopyrightLatch = new CountDownLatch(1);
-        hasLogStreamEnded = false;
+        logStreamClosedLatch = new CountDownLatch(1);
     }
 
     @Override
@@ -104,7 +104,7 @@ public class CppLogMessageHandler implements Closeable {
                 readBuf = new byte[readBufSize];
             }
         } finally {
-            hasLogStreamEnded = true;
+            logStreamClosedLatch.countDown();
 
             // check if there is some leftover from log summarization
             if (lastMessageSummary.count > 0) {
@@ -114,13 +114,22 @@ public class CppLogMessageHandler implements Closeable {
     }
 
     public boolean hasLogStreamEnded() {
-        return hasLogStreamEnded;
+        return logStreamClosedLatch.getCount() == 0;
     }
 
     public boolean seenFatalError() {
         return seenFatalError;
     }
 
+    public boolean waitForLogStreamClose(Duration timeout) {
+        try {
+            return logStreamClosedLatch.await(timeout.toMillis(), TimeUnit.MILLISECONDS);
+        } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
+        }
+        return false;
+    }
+
     /**
      * Get the process ID of the C++ process whose log messages are being read.  This will
      * arrive in the first log message logged by the C++ process.  They all log their version
diff --git a/plugin/src/test/java/org/elasticsearch/xpack/ml/job/process/logging/CppLogMessageHandlerTests.java b/plugin/src/test/java/org/elasticsearch/xpack/ml/job/process/logging/CppLogMessageHandlerTests.java
index 3cfcd5e32a1..96d9b66b15a 100644
--- a/plugin/src/test/java/org/elasticsearch/xpack/ml/job/process/logging/CppLogMessageHandlerTests.java
+++ b/plugin/src/test/java/org/elasticsearch/xpack/ml/job/process/logging/CppLogMessageHandlerTests.java
@@ -179,6 +179,17 @@ public class CppLogMessageHandlerTests extends ESTestCase {
         executeLoggingTest(is, mockAppender, Level.DEBUG);
     }
 
+    public void testWaitForLogStreamClose() throws IOException {
+        InputStream is = new ByteArrayInputStream(String.join("", TEST_MESSAGE_NOISE, TEST_MESSAGE_NOISE, TEST_MESSAGE_NOISE,
+                TEST_MESSAGE_NOISE, TEST_MESSAGE_NOISE, TEST_MESSAGE_NOISE_DIFFERENT_MESSAGE).getBytes(StandardCharsets.UTF_8));
+
+        try (CppLogMessageHandler handler = new CppLogMessageHandler("test_throttling", is)) {
+            handler.tailStream();
+            assertTrue(handler.waitForLogStreamClose(Duration.ofMillis(100)));
+            assertTrue(handler.hasLogStreamEnded());
+        }
+    }
+
     private static void executeLoggingTest(InputStream is, MockLogAppender mockAppender, Level level) throws IOException {
         Logger cppMessageLogger = Loggers.getLogger(CppLogMessageHandler.class);
         Loggers.addAppender(cppMessageLogger, mockAppender);