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 08a36aecbf..4456dad6c6 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
@@ -186,11 +186,30 @@ public final class EmulationActivity extends AppCompatActivity
     sIgnoreLaunchRequests = false;
   }
 
-  public static void clearWiimoteNewIniLinkedPreferences(Context context)
+  public static void updateWiimoteNewIniPreferences(Context context)
   {
-    SharedPreferences.Editor editor = PreferenceManager.getDefaultSharedPreferences(context).edit();
-    editor.remove("wiiController");
-    editor.apply();
+    SharedPreferences preferences = PreferenceManager.getDefaultSharedPreferences(context);
+    updateWiimoteNewController(preferences.getInt("wiiController", 3), context);
+
+    updateWiimoteNewImuIr(IntSetting.MAIN_MOTION_CONTROLS.getIntGlobal());
+  }
+
+  private static void updateWiimoteNewController(int value, Context context)
+  {
+    File wiimoteNewFile = SettingsFile.getSettingsFile(Settings.FILE_WIIMOTE);
+    IniFile wiimoteNewIni = new IniFile(wiimoteNewFile);
+    wiimoteNewIni.setString("Wiimote1", "Extension",
+            context.getResources().getStringArray(R.array.controllersValues)[value]);
+    wiimoteNewIni.setBoolean("Wiimote1", "Options/Sideways Wiimote", value == 2);
+    wiimoteNewIni.save(wiimoteNewFile);
+  }
+
+  private static void updateWiimoteNewImuIr(int value)
+  {
+    File wiimoteNewFile = SettingsFile.getSettingsFile(Settings.FILE_WIIMOTE);
+    IniFile wiimoteNewIni = new IniFile(wiimoteNewFile);
+    wiimoteNewIni.setBoolean("Wiimote1", "IMUIR/Enabled", value != 1);
+    wiimoteNewIni.save(wiimoteNewFile);
   }
 
   @Override
@@ -847,13 +866,7 @@ public final class EmulationActivity extends AppCompatActivity
             {
               editor.putInt("wiiController", indexSelected);
 
-              File wiimoteNewFile = SettingsFile.getSettingsFile(Settings.FILE_WIIMOTE);
-              IniFile wiimoteNewIni = new IniFile(wiimoteNewFile);
-              wiimoteNewIni.setString("Wiimote1", "Extension",
-                      getResources().getStringArray(R.array.controllersValues)[indexSelected]);
-              wiimoteNewIni.setBoolean("Wiimote1", "Options/Sideways Wiimote", indexSelected == 2);
-              wiimoteNewIni.save(wiimoteNewFile);
-
+              updateWiimoteNewController(indexSelected, this);
               NativeLibrary.ReloadWiimoteConfig();
             });
     builder.setPositiveButton(R.string.ok, (dialogInterface, i) ->
@@ -877,11 +890,7 @@ public final class EmulationActivity extends AppCompatActivity
 
               updateMotionListener();
 
-              File wiimoteNewFile = SettingsFile.getSettingsFile(Settings.FILE_WIIMOTE);
-              IniFile wiimoteNewIni = new IniFile(wiimoteNewFile);
-              wiimoteNewIni.setBoolean("Wiimote1", "IMUIR/Enabled", indexSelected != 1);
-              wiimoteNewIni.save(wiimoteNewFile);
-
+              updateWiimoteNewImuIr(indexSelected);
               NativeLibrary.ReloadWiimoteConfig();
             });
     builder.setPositiveButton(R.string.ok, (dialogInterface, i) -> dialogInterface.dismiss());
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 4e293dfc4a..fc699a8838 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
@@ -70,10 +70,17 @@ public final class DirectoryInitialization
         if (setDolphinUserDirectory(context))
         {
           initializeInternalStorage(context);
-          initializeExternalStorage(context);
+          boolean wiimoteIniWritten = initializeExternalStorage(context);
           NativeLibrary.Initialize();
           NativeLibrary.ReportStartToAnalytics();
 
+          if (wiimoteIniWritten)
+          {
+            // This has to be done after calling NativeLibrary.Initialize(),
+            // as it relies on the config system
+            EmulationActivity.updateWiimoteNewIniPreferences(context);
+          }
+
           directoryState = DirectoryInitializationState.DOLPHIN_DIRECTORIES_INITIALIZED;
         }
         else
@@ -137,7 +144,8 @@ public final class DirectoryInitialization
     SetSysDirectory(sysDirectory.getPath());
   }
 
-  private static void initializeExternalStorage(Context context)
+  // Returns whether the WiimoteNew.ini file was written to
+  private static boolean initializeExternalStorage(Context context)
   {
     // Create User directory structure and copy some NAND files from the extracted Sys directory.
     CreateUserDirectories();
@@ -159,21 +167,20 @@ public final class DirectoryInitialization
     copyAsset("GCPadNew.ini", new File(configDirectory, "GCPadNew.ini"), true, context);
 
     SharedPreferences prefs = PreferenceManager.getDefaultSharedPreferences(context);
-    if (prefs.getInt("WiimoteNewVersion", 0) != WiimoteNewVersion)
+    boolean overwriteWiimoteIni = prefs.getInt("WiimoteNewVersion", 0) != WiimoteNewVersion;
+    boolean wiimoteIniWritten = copyAsset("WiimoteNew.ini",
+            new File(configDirectory, "WiimoteNew.ini"), overwriteWiimoteIni, context);
+    if (overwriteWiimoteIni)
     {
-      EmulationActivity.clearWiimoteNewIniLinkedPreferences(context);
-      copyAsset("WiimoteNew.ini", new File(configDirectory, "WiimoteNew.ini"), true, context);
       SharedPreferences.Editor sPrefsEditor = prefs.edit();
       sPrefsEditor.putInt("WiimoteNewVersion", WiimoteNewVersion);
       sPrefsEditor.apply();
     }
-    else
-    {
-      copyAsset("WiimoteNew.ini", new File(configDirectory, "WiimoteNew.ini"), false, context);
-    }
 
     copyAsset("WiimoteProfile.ini", new File(profileDirectory, "WiimoteProfile.ini"), true,
             context);
+
+    return wiimoteIniWritten;
   }
 
   private static void deleteDirectoryRecursively(@NonNull final File file)
@@ -258,7 +265,7 @@ public final class DirectoryInitialization
     LocalBroadcastManager.getInstance(context).sendBroadcast(localIntent);
   }
 
-  private static void copyAsset(String asset, File output, Boolean overwrite, Context context)
+  private static boolean copyAsset(String asset, File output, Boolean overwrite, Context context)
   {
     Log.verbose("[DirectoryInitialization] Copying File " + asset + " to " + output);
 
@@ -266,11 +273,14 @@ public final class DirectoryInitialization
     {
       if (!output.exists() || overwrite)
       {
-        InputStream in = context.getAssets().open(asset);
-        OutputStream out = new FileOutputStream(output);
-        copyFile(in, out);
-        in.close();
-        out.close();
+        try (InputStream in = context.getAssets().open(asset))
+        {
+          try (OutputStream out = new FileOutputStream(output))
+          {
+            copyFile(in, out);
+            return true;
+          }
+        }
       }
     }
     catch (IOException e)
@@ -278,6 +288,7 @@ public final class DirectoryInitialization
       Log.error("[DirectoryInitialization] Failed to copy asset file: " + asset +
               e.getMessage());
     }
+    return false;
   }
 
   private static void copyAssetFolder(String assetFolder, File outputFolder, Boolean overwrite,