diff --git a/examples/java-matter-controller/BUILD.gn b/examples/java-matter-controller/BUILD.gn
index 154f75aba19227..9830b360195c1d 100644
--- a/examples/java-matter-controller/BUILD.gn
+++ b/examples/java-matter-controller/BUILD.gn
@@ -58,9 +58,6 @@ java_binary("java-matter-controller") {
     "java/src/com/matter/controller/commands/pairing/PairingModeType.java",
     "java/src/com/matter/controller/commands/pairing/PairingNetworkType.java",
     "java/src/com/matter/controller/commands/pairing/UnpairCommand.java",
-    "java/src/com/matter/controller/config/PersistentStorage.java",
-    "java/src/com/matter/controller/config/PersistentStorageOpCertStore.java",
-    "java/src/com/matter/controller/config/PersistentStorageOperationalKeystore.java",
   ]
 
   javac_flags = [ "-Xlint:deprecation" ]
diff --git a/examples/java-matter-controller/java/src/com/matter/controller/commands/common/MatterCommand.java b/examples/java-matter-controller/java/src/com/matter/controller/commands/common/MatterCommand.java
index 5336ce8f24a991..b892c0bf678282 100644
--- a/examples/java-matter-controller/java/src/com/matter/controller/commands/common/MatterCommand.java
+++ b/examples/java-matter-controller/java/src/com/matter/controller/commands/common/MatterCommand.java
@@ -19,21 +19,12 @@
 package com.matter.controller.commands.common;
 
 import chip.devicecontroller.ChipDeviceController;
-import com.matter.controller.config.PersistentStorage;
-import com.matter.controller.config.PersistentStorageOpCertStore;
-import com.matter.controller.config.PersistentStorageOperationalKeystore;
 import java.util.Optional;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicLong;
 
 public abstract class MatterCommand extends Command {
   private final ChipDeviceController mChipDeviceController;
-  private final PersistentStorage mDefaultStorage = new PersistentStorage();
-  private final PersistentStorage mCommissionerStorage = new PersistentStorage();
-  private final PersistentStorageOperationalKeystore mOperationalKeystore =
-      new PersistentStorageOperationalKeystore();
-  private final PersistentStorageOpCertStore mOpCertStore = new PersistentStorageOpCertStore();
-
   private final Optional<CredentialsIssuer> mCredIssuerCmds;
   private final StringBuffer mCommissionerName = new StringBuffer();
   private final StringBuffer mPaaTrustStorePath = new StringBuffer();
@@ -104,24 +95,11 @@ public ChipDeviceController currentCommissioner() {
   /////////// Command Interface /////////
   @Override
   public void run() throws Exception {
-    // TODO: setup chip storage from Java, currently it is using example one from chip-tool
-    // maybeSetUpStack();
     runCommand();
-    // maybeTearDownStack();
   }
 
   protected abstract void runCommand();
 
-  private void maybeSetUpStack() throws Exception {
-    mDefaultStorage.init();
-    mOperationalKeystore.init(mDefaultStorage);
-    mOpCertStore.init(mDefaultStorage);
-  }
-
-  private void maybeTearDownStack() {
-    // ToDo:We need to call DeviceController::Shutdown()
-  }
-
   public void setTestResult(String result) {
     mTestResult = Optional.of(result);
   }
diff --git a/examples/java-matter-controller/java/src/com/matter/controller/config/PersistentStorage.java b/examples/java-matter-controller/java/src/com/matter/controller/config/PersistentStorage.java
deleted file mode 100644
index eea19943ddf83c..00000000000000
--- a/examples/java-matter-controller/java/src/com/matter/controller/config/PersistentStorage.java
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- *   Copyright (c) 2022 Project CHIP Authors
- *   All rights reserved.
- *
- *   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.matter.controller.config;
-
-public class PersistentStorage {
-  public void init() throws Exception {
-    throw new Exception("Failed to initialize PersistentStorage");
-  }
-}
diff --git a/examples/java-matter-controller/java/src/com/matter/controller/config/PersistentStorageOpCertStore.java b/examples/java-matter-controller/java/src/com/matter/controller/config/PersistentStorageOpCertStore.java
deleted file mode 100644
index 04b5617e799c39..00000000000000
--- a/examples/java-matter-controller/java/src/com/matter/controller/config/PersistentStorageOpCertStore.java
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- *   Copyright (c) 2022 Project CHIP Authors
- *   All rights reserved.
- *
- *   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.matter.controller.config;
-
-public class PersistentStorageOpCertStore {
-  public int init(PersistentStorage storage) throws Exception {
-    throw new Exception("Failed to initialize PersistentStorageOpCertStore");
-  }
-}
diff --git a/examples/java-matter-controller/java/src/com/matter/controller/config/PersistentStorageOperationalKeystore.java b/examples/java-matter-controller/java/src/com/matter/controller/config/PersistentStorageOperationalKeystore.java
deleted file mode 100644
index 819a129af27448..00000000000000
--- a/examples/java-matter-controller/java/src/com/matter/controller/config/PersistentStorageOperationalKeystore.java
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- *   Copyright (c) 2022 Project CHIP Authors
- *   All rights reserved.
- *
- *   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.matter.controller.config;
-
-public class PersistentStorageOperationalKeystore {
-  public int init(PersistentStorage storage) throws Exception {
-    throw new Exception("Failed to initialize PersistentStorageOperationalKeystore");
-  }
-}