diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/DolphinApplication.java b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/DolphinApplication.java
index e0eb5e5415..6c2e3be39d 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/DolphinApplication.java
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/DolphinApplication.java
@@ -3,6 +3,8 @@ package org.dolphinemu.dolphinemu;
 import android.app.Application;
 
 import org.dolphinemu.dolphinemu.model.GameDatabase;
+import org.dolphinemu.dolphinemu.services.DirectoryInitializationService;
+import org.dolphinemu.dolphinemu.utils.PermissionsHandler;
 
 public class DolphinApplication extends Application
 {
@@ -13,6 +15,11 @@ public class DolphinApplication extends Application
 	{
 		super.onCreate();
 
+		NativeLibrary.SetUserDirectory("");  // Empty string means use the default path
+
+		if (PermissionsHandler.hasWriteAccess(getApplicationContext()))
+			DirectoryInitializationService.startService(getApplicationContext());
+
 		databaseHelper = new GameDatabase(this);
 	}
 }
diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/MainActivity.java b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/MainActivity.java
index 72a9477f00..1f46f8eecb 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/MainActivity.java
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/MainActivity.java
@@ -58,7 +58,6 @@ public final class MainActivity extends AppCompatActivity implements MainView
 		mPresenter.onCreate();
 
 		// Stuff in this block only happens when this activity is newly created (i.e. not a rotation)
-		// TODO Split some of this stuff into Application.onCreate()
 		if (savedInstanceState == null)
 			StartupHandler.HandleInit(this);
 
diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/StartupHandler.java b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/StartupHandler.java
index 11cdf861c6..738d696b31 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/StartupHandler.java
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/StartupHandler.java
@@ -5,28 +5,19 @@ import android.os.Bundle;
 import android.support.v4.app.FragmentActivity;
 import android.text.TextUtils;
 
-import org.dolphinemu.dolphinemu.NativeLibrary;
 import org.dolphinemu.dolphinemu.activities.EmulationActivity;
-import org.dolphinemu.dolphinemu.services.DirectoryInitializationService;
 
 public final class StartupHandler
 {
 	public static boolean HandleInit(FragmentActivity parent)
 	{
-		String user_dir = "";
-		String start_file = "";
+		// Ask the user to grant write permission if it's not already granted
+		PermissionsHandler.checkWritePermission(parent);
 
+		String start_file = "";
 		Bundle extras = parent.getIntent().getExtras();
 		if (extras != null)
-		{
-			user_dir = extras.getString("UserDir");
 			start_file = extras.getString("AutoStartFile");
-		}
-
-		NativeLibrary.SetUserDirectory(user_dir);  // Uses default path if user_dir equals ""
-
-		if (PermissionsHandler.checkWritePermission(parent))
-			DirectoryInitializationService.startService(parent);
 
 		if (!TextUtils.isEmpty(start_file))
 		{