diff --git a/sdks/java/io/kafka/src/main/java/org/apache/beam/sdk/io/kafka/KafkaIO.java b/sdks/java/io/kafka/src/main/java/org/apache/beam/sdk/io/kafka/KafkaIO.java
index 4f353df865ff..3d228242b8a5 100644
--- a/sdks/java/io/kafka/src/main/java/org/apache/beam/sdk/io/kafka/KafkaIO.java
+++ b/sdks/java/io/kafka/src/main/java/org/apache/beam/sdk/io/kafka/KafkaIO.java
@@ -81,6 +81,7 @@
 import java.util.concurrent.ScheduledExecutorService;
 import java.util.concurrent.SynchronousQueue;
 import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 import javax.annotation.Nullable;
 
@@ -686,7 +687,7 @@ private static class UnboundedKafkaReader<K, V> extends UnboundedReader<KafkaRec
     private final ExecutorService consumerPollThread = Executors.newSingleThreadExecutor();
     private final SynchronousQueue<ConsumerRecords<byte[], byte[]>> availableRecordsQueue =
         new SynchronousQueue<>();
-    private volatile boolean closed = false;
+    private AtomicBoolean closed = new AtomicBoolean(false);
 
     // Backlog support :
     // Kafka consumer does not have an API to fetch latest offset for topic. We need to seekToEnd()
@@ -792,10 +793,10 @@ public PartitionState apply(TopicPartition tp) {
 
     private void consumerPollLoop() {
       // Read in a loop and enqueue the batch of records, if any, to availableRecordsQueue
-      while (!closed) {
+      while (!closed.get()) {
         try {
           ConsumerRecords<byte[], byte[]> records = consumer.poll(KAFKA_POLL_TIMEOUT.getMillis());
-          if (!records.isEmpty()) {
+          if (!records.isEmpty() && !closed.get()) {
             availableRecordsQueue.put(records); // blocks until dequeued.
           }
         } catch (InterruptedException e) {
@@ -817,6 +818,7 @@ private void nextBatch() {
         records = availableRecordsQueue.poll(NEW_RECORDS_POLL_TIMEOUT.getMillis(),
                                              TimeUnit.MILLISECONDS);
       } catch (InterruptedException e) {
+        Thread.currentThread().interrupt();
         LOG.warn("{}: Unexpected", this, e);
         return;
       }
@@ -1041,11 +1043,32 @@ public long getSplitBacklogBytes() {
 
     @Override
     public void close() throws IOException {
-      closed = true;
-      availableRecordsQueue.poll(); // drain unread batch, this unblocks consumer thread.
-      consumer.wakeup();
+      closed.set(true);
       consumerPollThread.shutdown();
       offsetFetcherThread.shutdown();
+
+      boolean isShutdown = false;
+
+      // Wait for threads to shutdown. Trying this a loop to handle a tiny race where poll thread
+      // might block to enqueue right after availableRecordsQueue.poll() below.
+      while (!isShutdown) {
+
+        consumer.wakeup();
+        offsetConsumer.wakeup();
+        availableRecordsQueue.poll(); // drain unread batch, this unblocks consumer thread.
+        try {
+          isShutdown = consumerPollThread.awaitTermination(10, TimeUnit.SECONDS)
+              && offsetFetcherThread.awaitTermination(10, TimeUnit.SECONDS);
+        } catch (InterruptedException e) {
+          Thread.currentThread().interrupt();
+          throw new RuntimeException(e); // not expected
+        }
+
+        if (!isShutdown) {
+          LOG.warn("An internal thread is taking a long time to shutdown. will retry.");
+        }
+      }
+
       Closeables.close(offsetConsumer, true);
       Closeables.close(consumer, true);
     }