diff --git a/gerrit-acceptance-tests/src/test/java/com/google/gerrit/acceptance/pgm/RebuildNotedbIT.java b/gerrit-acceptance-tests/src/test/java/com/google/gerrit/acceptance/pgm/RebuildNotedbIT.java
new file mode 100644
index 0000000000..c538b85d82
--- /dev/null
+++ b/gerrit-acceptance-tests/src/test/java/com/google/gerrit/acceptance/pgm/RebuildNotedbIT.java
@@ -0,0 +1,64 @@
+// Copyright (C) 2014 The Android Open Source Project
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package com.google.gerrit.acceptance.pgm;
+
+import static com.google.common.truth.Truth.assertThat;
+
+import com.google.common.io.Files;
+import com.google.gerrit.launcher.GerritLauncher;
+import com.google.gerrit.server.notedb.NotesMigration;
+import com.google.gerrit.testutil.TempFileUtil;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.nio.charset.StandardCharsets;
+
+public class RebuildNotedbIT {
+  private File sitePath;
+
+  @Before
+  public void createTempDirectory() throws Exception {
+    sitePath = TempFileUtil.createTempDirectory();
+  }
+
+  @After
+  public void destroySite() throws Exception {
+    if (sitePath != null) {
+      TempFileUtil.cleanup();
+    }
+  }
+
+  @Test
+  public void rebuildEmptySite() throws Exception {
+    initSite();
+    Files.append(NotesMigration.allEnabledConfig().toText(),
+        new File(sitePath.toString(), "etc/gerrit.config"),
+        StandardCharsets.UTF_8);
+    runGerrit("RebuildNotedb", "-d", sitePath.toString(),
+        "--show-stack-trace");
+  }
+
+  private void initSite() throws Exception {
+    runGerrit("init", "-d", sitePath.getPath(),
+        "--batch", "--no-auto-start", "--skip-plugins", "--show-stack-trace");
+  }
+
+  private static void runGerrit(String... args) throws Exception {
+    assertThat(GerritLauncher.mainImpl(args)).isEqualTo(0);
+  }
+}
diff --git a/gerrit-pgm/src/main/java/com/google/gerrit/pgm/RebuildNotedb.java b/gerrit-pgm/src/main/java/com/google/gerrit/pgm/RebuildNotedb.java
index 4593aef1dd..afbb91806a 100644
--- a/gerrit-pgm/src/main/java/com/google/gerrit/pgm/RebuildNotedb.java
+++ b/gerrit-pgm/src/main/java/com/google/gerrit/pgm/RebuildNotedb.java
@@ -25,8 +25,10 @@ import com.google.common.util.concurrent.Futures;
 import com.google.common.util.concurrent.ListenableFuture;
 import com.google.common.util.concurrent.ListeningExecutorService;
 import com.google.common.util.concurrent.MoreExecutors;
+import com.google.gerrit.extensions.events.GitReferenceUpdatedListener;
+import com.google.gerrit.extensions.registration.DynamicSet;
 import com.google.gerrit.lifecycle.LifecycleManager;
-import com.google.gerrit.pgm.util.BatchGitModule;
+import com.google.gerrit.lucene.LuceneIndexModule;
 import com.google.gerrit.pgm.util.BatchProgramModule;
 import com.google.gerrit.pgm.util.SiteProgram;
 import com.google.gerrit.pgm.util.ThreadLimiter;
@@ -39,14 +41,18 @@ import com.google.gerrit.server.git.GitRepositoryManager;
 import com.google.gerrit.server.git.MultiProgressMonitor;
 import com.google.gerrit.server.git.MultiProgressMonitor.Task;
 import com.google.gerrit.server.git.WorkQueue;
+import com.google.gerrit.server.index.IndexModule;
+import com.google.gerrit.server.index.ReindexAfterUpdate;
 import com.google.gerrit.server.notedb.ChangeRebuilder;
 import com.google.gerrit.server.notedb.NoteDbModule;
 import com.google.gerrit.server.notedb.NotesMigration;
+import com.google.gerrit.solr.SolrIndexModule;
 import com.google.gwtorm.server.OrmException;
 import com.google.gwtorm.server.SchemaFactory;
 import com.google.inject.AbstractModule;
 import com.google.inject.Injector;
 import com.google.inject.Key;
+import com.google.inject.Module;
 import com.google.inject.TypeLiteral;
 
 import org.eclipse.jgit.lib.BatchRefUpdate;
@@ -205,8 +211,21 @@ public class RebuildNotedb extends SiteProgram {
       @Override
       public void configure() {
         install(dbInjector.getInstance(BatchProgramModule.class));
-        install(new BatchGitModule());
         install(new NoteDbModule());
+        DynamicSet.bind(binder(), GitReferenceUpdatedListener.class).to(
+            ReindexAfterUpdate.class);
+        Module changeIndexModule;
+        switch (IndexModule.getIndexType(dbInjector)) {
+          case LUCENE:
+            changeIndexModule = new LuceneIndexModule(null, threads, null);
+            break;
+          case SOLR:
+            changeIndexModule = new SolrIndexModule(false, threads, null);
+            break;
+          default:
+            throw new IllegalStateException("unsupported index.type");
+        }
+        install(changeIndexModule);
       }
     });
   }