diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/activities/EmulationActivity.java b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/activities/EmulationActivity.java
index 8577158706..334ecb671c 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/activities/EmulationActivity.java
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/activities/EmulationActivity.java
@@ -1,5 +1,6 @@
 package org.dolphinemu.dolphinemu.activities;
 
+import android.content.Context;
 import android.content.DialogInterface;
 import android.content.Intent;
 import android.content.SharedPreferences;
@@ -237,6 +238,14 @@ public final class EmulationActivity extends AppCompatActivity
     activity.startActivity(launcher);
   }
 
+  public static void clearWiimoteNewIniLinkedPreferences(Context context)
+  {
+    SharedPreferences.Editor editor = PreferenceManager.getDefaultSharedPreferences(context).edit();
+    editor.remove("wiiController");
+    editor.remove("motionControlsEnabled");
+    editor.apply();
+  }
+
   @Override
   protected void onCreate(Bundle savedInstanceState)
   {
diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/DirectoryInitialization.java b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/DirectoryInitialization.java
index 7742ac90ae..45b3c69155 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/DirectoryInitialization.java
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/DirectoryInitialization.java
@@ -15,6 +15,7 @@ import android.preference.PreferenceManager;
 import androidx.localbroadcastmanager.content.LocalBroadcastManager;
 
 import org.dolphinemu.dolphinemu.NativeLibrary;
+import org.dolphinemu.dolphinemu.activities.EmulationActivity;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -152,6 +153,7 @@ public final class DirectoryInitialization
     SharedPreferences prefs = PreferenceManager.getDefaultSharedPreferences(context);
     if (prefs.getInt("WiimoteNewVersion", 0) != WiimoteNewVersion)
     {
+      EmulationActivity.clearWiimoteNewIniLinkedPreferences(context);
       copyAsset("WiimoteNew.ini", new File(configDirectory, "WiimoteNew.ini"), true, context);
       SharedPreferences.Editor sPrefsEditor = prefs.edit();
       sPrefsEditor.putInt("WiimoteNewVersion", WiimoteNewVersion);