diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/plugins/document/util/MapDBMapFactory.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/plugins/document/util/MapDBMapFactory.java
index fefd19eda7..0cb71944f4 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/plugins/document/util/MapDBMapFactory.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/plugins/document/util/MapDBMapFactory.java
@@ -43,7 +43,6 @@
     public MapDBMapFactory() {
         this.db = DBMaker.newTempFileDB()
                 .deleteFilesAfterClose()
-                .closeOnJvmShutdown()
                 .transactionDisable()
                 .asyncWriteEnable()
                 .make();
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/CheckpointsCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/CheckpointsCommand.java
index 28553565f4..a63fb1bf4a 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/CheckpointsCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/CheckpointsCommand.java
@@ -50,7 +50,7 @@ public void execute(String... args) throws Exception {
 
         boolean success = false;
         Checkpoints cps;
-        Closer closer = Closer.create();
+        Closer closer = Utils.createCloserWithShutdownHook();
         try {
             String op = "list";
             if (options.nonOptionArguments().size() >= 2) {
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/ClusterNodesCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/ClusterNodesCommand.java
index 190f9db637..d93eafe100 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/ClusterNodesCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/ClusterNodesCommand.java
@@ -42,7 +42,7 @@
 
     @Override
     public void execute(String... args) throws Exception {
-        Closer closer = Closer.create();
+        Closer closer = Utils.createCloserWithShutdownHook();
         try {
             String h = "clusternodes mongodb://host:port/database|jdbc:...";
             ClusterNodesOptions options = new ClusterNodesOptions(h).parse(args);
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCheckCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCheckCommand.java
index 4762c6666c..6eb1c5d7c3 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCheckCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCheckCommand.java
@@ -119,7 +119,7 @@ static int checkDataStore(String... args) {
                 + "[--s3ds <s3ds_config>|--fds <fds_config>|--azureblobds <azureblobds_config>|--nods]"
                 + " [--dump <path>] [--repoHome <repo_home>] [--track] [--verbose]";
 
-        try (Closer closer = Closer.create()) {
+        try (Closer closer = Utils.createCloserWithShutdownHook()) {
             // Options for operations requested
             OptionSpecBuilder idOp = parser.accepts("id", "Get ids");
             OptionSpecBuilder refOp = parser.accepts("ref", "Get references");
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCommand.java
index 6f50f973e6..36efa43699 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCommand.java
@@ -108,7 +108,7 @@ public void execute(String... args) throws Exception {
         logCliArgs(args);
 
         boolean success = false;
-        try (Closer closer = Closer.create()) {
+        try (Closer closer = Utils.createCloserWithShutdownHook()) {
             opts.setTempDirectory(dataStoreOpts.getWorkDir().getAbsolutePath());
             NodeStoreFixture fixture = NodeStoreFixtureProvider.create(opts);
             closer.register(fixture);
@@ -152,7 +152,7 @@ private static boolean checkParameters(DataStoreOptions dataStoreOpts, Options o
     private void execute(NodeStoreFixture fixture,  DataStoreOptions dataStoreOpts, Options opts, Closer closer)
         throws Exception {
 
-        try (Closer metricsCloser = Closer.create()) {
+        try (Closer metricsCloser = Utils.createCloserWithShutdownHook()) {
             MetricsExporterFixture metricsExporterFixture =
                 MetricsExporterFixtureProvider.create(dataStoreOpts, fixture.getWhiteboard());
             metricsCloser.register(metricsExporterFixture);
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/GarbageCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/GarbageCommand.java
index 9e2deb4bea..4787f65676 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/GarbageCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/GarbageCommand.java
@@ -27,7 +27,7 @@
 
     @Override
     public void execute(String... args) throws Exception {
-        Closer closer = Closer.create();
+        Closer closer = Utils.createCloserWithShutdownHook();
         String h = "garbage mongodb://host:port/database | jdbc:...";
         try {
             NodeStore store = Utils.bootstrapNodeStore(args, closer, h);
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RecoveryCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RecoveryCommand.java
index 633c407c34..c8c1d9112c 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RecoveryCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RecoveryCommand.java
@@ -44,7 +44,7 @@
     @Override
     public void execute(String... args) throws Exception {
         MapFactory.setInstance(new MapDBMapFactory());
-        Closer closer = Closer.create();
+        Closer closer = Utils.createCloserWithShutdownHook();
         String h = "recovery mongodb://host:port/database|jdbc:... { dryRun }";
 
         try {
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RepairCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RepairCommand.java
index 27198b12bd..c84ed47eee 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RepairCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RepairCommand.java
@@ -28,7 +28,7 @@
 
     @Override
     public void execute(String... args) throws Exception {
-        Closer closer = Closer.create();
+        Closer closer = Utils.createCloserWithShutdownHook();
         String h = "repair mongodb://host:port/database path";
         try {
             NodeStore store = Utils.bootstrapNodeStore(args, closer, h);
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/ResetClusterIdCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/ResetClusterIdCommand.java
index b3a8d6588a..4c4ee993c0 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/ResetClusterIdCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/ResetClusterIdCommand.java
@@ -76,7 +76,7 @@ public void execute(String... args) throws Exception {
         String help = "resetclusterid {<path>|<mongo-uri>|<jdbc-uri>}";
         Utils.NodeStoreOptions opts = new Utils.NodeStoreOptions(help).parse(args);
 
-        Closer closer = Closer.create();
+        Closer closer = Utils.createCloserWithShutdownHook();
         try {
             NodeStore store = Utils.bootstrapNodeStore(opts, closer);
             deleteClusterId(store);
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RevisionsCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RevisionsCommand.java
index 21e5aff706..b572450a4d 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RevisionsCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/RevisionsCommand.java
@@ -166,7 +166,7 @@ boolean isVerbose() {
 
     @Override
     public void execute(String... args) throws Exception {
-        Closer closer = Closer.create();
+        Closer closer = Utils.createCloserWithShutdownHook();
         try {
             RevisionsOptions options = new RevisionsOptions(USAGE).parse(args);
             setupLoggers(options.isVerbose());
diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/Utils.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/Utils.java
index 9bca819840..bff255a6c4 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/Utils.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/Utils.java
@@ -341,6 +341,19 @@ public void close() throws IOException {
         };
     }
 
+    static Closer createCloserWithShutdownHook() {
+        Closer closer = Closer.create();
+        Runtime.getRuntime().addShutdownHook(new Thread() {
+            public void run() {
+                try {
+                    closer.close();
+                } catch (IOException e) {
+                    e.printStackTrace(System.err);
+                }
+            }
+        });
+        return closer;
+    }
 
     private static Properties loadAndTransformProps(String cfgPath) throws IOException {
         Dictionary dict = ConfigurationHandler.read(new FileInputStream(cfgPath));