diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/control/FinalizeBundleHandler.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/control/FinalizeBundleHandler.java
index d3e9eddf75aa..13bb8ceae05d 100644
--- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/control/FinalizeBundleHandler.java
+++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/control/FinalizeBundleHandler.java
@@ -24,11 +24,15 @@
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.PriorityQueue;
-import java.util.concurrent.Callable;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentMap;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.locks.Condition;
+import java.util.concurrent.locks.ReentrantLock;
+import javax.annotation.Nullable;
+import javax.annotation.concurrent.GuardedBy;
 import org.apache.beam.model.fnexecution.v1.BeamFnApi;
 import org.apache.beam.model.fnexecution.v1.BeamFnApi.FinalizeBundleResponse;
 import org.apache.beam.sdk.transforms.DoFn.BundleFinalizer;
@@ -45,14 +49,11 @@
  * <p>See <a href="https://s.apache.org/beam-finalizing-bundles">Apache Beam Portability API: How to
  * Finalize Bundles</a> for further details.
  */
-@SuppressWarnings({
-  "nullness" // TODO(https://github.com/apache/beam/issues/20497)
-})
 public class FinalizeBundleHandler {
 
   /** A {@link BundleFinalizer.Callback} and expiry time pair. */
   @AutoValue
-  abstract static class CallbackRegistration {
+  public abstract static class CallbackRegistration {
     public static CallbackRegistration create(
         Instant expiryTime, BundleFinalizer.Callback callback) {
       return new AutoValue_FinalizeBundleHandler_CallbackRegistration(expiryTime, callback);
@@ -64,55 +65,53 @@ public static CallbackRegistration create(
   }
 
   private final ConcurrentMap<String, Collection<CallbackRegistration>> bundleFinalizationCallbacks;
+  private final ReentrantLock cleanupLock = new ReentrantLock();
+  private final Condition queueMinChanged = cleanupLock.newCondition();
+
+  @GuardedBy("cleanupLock")
   private final PriorityQueue<TimestampedValue<String>> cleanUpQueue;
 
   @SuppressWarnings("unused")
-  private final Future<Void> cleanUpResult;
+  private final Future<?> cleanUpResult;
 
+  @SuppressWarnings("methodref.receiver.bound")
   public FinalizeBundleHandler(ExecutorService executorService) {
     this.bundleFinalizationCallbacks = new ConcurrentHashMap<>();
     this.cleanUpQueue =
         new PriorityQueue<>(11, Comparator.comparing(TimestampedValue::getTimestamp));
-    // Wait until we have at least one element. We are notified on each element
-    // being added.
-    // Wait until the current time has past the expiry time for the head of the
-    // queue.
-    // We are notified on each element being added.
-    // Wait until we have at least one element. We are notified on each element
-    // being added.
-    // Wait until the current time has past the expiry time for the head of the
-    // queue.
-    // We are notified on each element being added.
-    cleanUpResult =
-        executorService.submit(
-            (Callable<Void>)
-                () -> {
-                  while (true) {
-                    synchronized (cleanUpQueue) {
-                      TimestampedValue<String> expiryTime = cleanUpQueue.peek();
-
-                      // Wait until we have at least one element. We are notified on each element
-                      // being added.
-                      while (expiryTime == null) {
-                        cleanUpQueue.wait();
-                        expiryTime = cleanUpQueue.peek();
-                      }
-
-                      // Wait until the current time has past the expiry time for the head of the
-                      // queue.
-                      // We are notified on each element being added.
-                      Instant now = Instant.now();
-                      while (expiryTime.getTimestamp().isAfter(now)) {
-                        Duration timeDifference = new Duration(now, expiryTime.getTimestamp());
-                        cleanUpQueue.wait(timeDifference.getMillis());
-                        expiryTime = cleanUpQueue.peek();
-                        now = Instant.now();
-                      }
-
-                      bundleFinalizationCallbacks.remove(cleanUpQueue.poll().getValue());
-                    }
-                  }
-                });
+
+    cleanUpResult = executorService.submit(this::cleanupThreadBody);
+  }
+
+  private void cleanupThreadBody() {
+    cleanupLock.lock();
+    try {
+      while (true) {
+        final @Nullable TimestampedValue<String> minValue = cleanUpQueue.peek();
+        if (minValue == null) {
+          // Wait for an element to be added and loop to re-examine the min.
+          queueMinChanged.await();
+          continue;
+        }
+
+        Instant now = Instant.now();
+        Duration timeDifference = new Duration(now, minValue.getTimestamp());
+        if (timeDifference.getMillis() > 0
+            && queueMinChanged.await(timeDifference.getMillis(), TimeUnit.MILLISECONDS)) {
+          // If the time didn't elapse, loop to re-examine the min.
+          continue;
+        }
+
+        // The minimum element has an expiry time before now.
+        // It may or may not actually be present in the map if the finalization has already been
+        // completed.
+        bundleFinalizationCallbacks.remove(minValue.getValue());
+      }
+    } catch (InterruptedException e) {
+      // We're being shutdown.
+    } finally {
+      cleanupLock.unlock();
+    }
   }
 
   public void registerCallbacks(String bundleId, Collection<CallbackRegistration> callbacks) {
@@ -131,9 +130,18 @@ public void registerCallbacks(String bundleId, Collection<CallbackRegistration>
     for (CallbackRegistration callback : callbacks) {
       expiryTimeMillis = Math.max(expiryTimeMillis, callback.getExpiryTime().getMillis());
     }
-    synchronized (cleanUpQueue) {
-      cleanUpQueue.offer(TimestampedValue.of(bundleId, new Instant(expiryTimeMillis)));
-      cleanUpQueue.notify();
+
+    cleanupLock.lock();
+    try {
+      TimestampedValue<String> value = TimestampedValue.of(bundleId, new Instant(expiryTimeMillis));
+      cleanUpQueue.offer(value);
+      @SuppressWarnings("ReferenceEquality")
+      boolean newMin = cleanUpQueue.peek() == value;
+      if (newMin) {
+        queueMinChanged.signal();
+      }
+    } finally {
+      cleanupLock.unlock();
     }
   }
 
@@ -141,13 +149,15 @@ public BeamFnApi.InstructionResponse.Builder finalizeBundle(BeamFnApi.Instructio
       throws Exception {
     String bundleId = request.getFinalizeBundle().getInstructionId();
 
-    Collection<CallbackRegistration> callbacks = bundleFinalizationCallbacks.remove(bundleId);
+    final @Nullable Collection<CallbackRegistration> callbacks =
+        bundleFinalizationCallbacks.remove(bundleId);
 
     if (callbacks == null) {
       // We have already processed the callbacks on a prior bundle finalization attempt
       return BeamFnApi.InstructionResponse.newBuilder()
           .setFinalizeBundle(FinalizeBundleResponse.getDefaultInstance());
     }
+    // We don't bother removing from the cleanupQueue.
 
     Collection<Exception> failures = new ArrayList<>();
     for (CallbackRegistration callback : callbacks) {