diff --git a/mist-core/src/main/java/edu/snu/mist/core/master/DefaultSharedStoreManagerImpl.java b/mist-core/src/main/java/edu/snu/mist/core/master/DefaultSharedStoreManagerImpl.java
new file mode 100644
index 00000000..961f0962
--- /dev/null
+++ b/mist-core/src/main/java/edu/snu/mist/core/master/DefaultSharedStoreManagerImpl.java
@@ -0,0 +1,61 @@
+/*
+ * Copyright (C) 2018 Seoul National University
+ *
+ * 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 edu.snu.mist.core.master;
+
+import edu.snu.mist.core.parameters.SharedStorePath;
+import org.apache.reef.tang.annotations.Parameter;
+
+import javax.inject.Inject;
+import java.io.File;
+
+/**
+ * The default shared store manager implementation class.
+ */
+public final class DefaultSharedStoreManagerImpl implements SharedStoreManager {
+
+  /**
+   * The shared store path.
+   */
+  private final String sharedStorePath;
+
+  @Inject
+  private DefaultSharedStoreManagerImpl(@Parameter(SharedStorePath.class) final String sharedStorePath) {
+    this.sharedStorePath = sharedStorePath;
+  }
+
+  @Override
+  public boolean clearSharedStore() {
+    final File sharedStoreDir = new File(sharedStorePath);
+    final File[] listing = sharedStoreDir.listFiles();
+    if (listing == null) {
+      throw new RuntimeException("Inavlid shared store directory path. Terminate MIST...");
+    }
+    if (listing.length == 0) {
+      return true;
+    }
+    for (final File file: listing) {
+      final String fileName = file.getName();
+      if (fileName.endsWith(".checkpoint") || fileName.endsWith(".query") || fileName.endsWith(".querylist")) {
+        // Try to delete the already existing query and checkpoint files...
+        if (!file.delete()) {
+          // If we fail to delete the existing files, there should be problems with the shared store...
+          return false;
+        }
+      }
+    }
+    return true;
+  }
+}
diff --git a/mist-core/src/main/java/edu/snu/mist/core/master/MistMaster.java b/mist-core/src/main/java/edu/snu/mist/core/master/MistMaster.java
index 62e0a200..6565a504 100644
--- a/mist-core/src/main/java/edu/snu/mist/core/master/MistMaster.java
+++ b/mist-core/src/main/java/edu/snu/mist/core/master/MistMaster.java
@@ -75,6 +75,11 @@ public final class MistMaster implements Task {
    */
   private final ApplicationCodeManager applicationCodeManager;
 
+  /**
+   * The shared store manager.
+   */
+  private final SharedStoreManager sharedStoreManager;
+
   @Inject
   private MistMaster(
       @Parameter(DriverToMasterPort.class) final int driverToMasterPort,
@@ -88,13 +93,15 @@ private MistMaster(
       final MasterSetupFinished masterSetupFinished,
       @Parameter(MasterRecovery.class) final boolean masterRecovery,
       final ApplicationCodeManager applicationCodeManager,
-      final DynamicScalingManager dynamicScalingManager) throws Exception {
+      final DynamicScalingManager dynamicScalingManager,
+      final SharedStoreManager sharedStoreManager) throws Exception {
     this.initialTaskNum = initialTaskNum;
     this.taskRequestor = taskRequestor;
     this.masterSetupFinished = masterSetupFinished;
     this.masterRecovery = masterRecovery;
     this.applicationCodeManager = applicationCodeManager;
     this.dynamicScalingManager = dynamicScalingManager;
+    this.sharedStoreManager = sharedStoreManager;
 
     // Initialize countdown latch
     this.countDownLatch = new CountDownLatch(1);
@@ -114,6 +121,10 @@ public byte[] call(final byte[] memento) throws Exception {
     if (!masterRecovery) {
       taskRequestor.setupTaskAndConn(initialTaskNum);
       masterSetupFinished.setFinished();
+      // Clear the shared store when the master is initiated for the first time.
+      if (!sharedStoreManager.clearSharedStore()) {
+        throw new RuntimeException("Cannot clear the shared store.. shutting down MIST...");
+      }
     } else {
       applicationCodeManager.recoverAppJarInfo();
       taskRequestor.recoverTaskConn();
diff --git a/mist-core/src/main/java/edu/snu/mist/core/master/SharedStoreManager.java b/mist-core/src/main/java/edu/snu/mist/core/master/SharedStoreManager.java
new file mode 100644
index 00000000..b00e88f3
--- /dev/null
+++ b/mist-core/src/main/java/edu/snu/mist/core/master/SharedStoreManager.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright (C) 2018 Seoul National University
+ *
+ * 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 edu.snu.mist.core.master;
+
+import org.apache.reef.tang.annotations.DefaultImplementation;
+
+/**
+ * The interface for master-side. shared store manager
+ */
+@DefaultImplementation(DefaultSharedStoreManagerImpl.class)
+public interface SharedStoreManager {
+
+  /**
+   * Clear the legacy query and checkpoint files on the shared store.
+   */
+  boolean clearSharedStore();
+}