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..1be60cd21f 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)
+	public static void 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))
 		{
@@ -35,9 +26,6 @@ public final class StartupHandler
 			emulation_intent.putExtra("SelectedGame", start_file);
 			parent.startActivity(emulation_intent);
 			parent.finish();
-			return false;
 		}
-
-		return false;
 	}
 }
diff --git a/Source/Android/jni/MainAndroid.cpp b/Source/Android/jni/MainAndroid.cpp
index 9fc8781cfa..c6c40da097 100644
--- a/Source/Android/jni/MainAndroid.cpp
+++ b/Source/Android/jni/MainAndroid.cpp
@@ -54,7 +54,6 @@ JavaVM* g_java_vm;
 namespace
 {
 ANativeWindow* s_surf;
-std::string s_set_userpath;
 
 jclass s_jni_class;
 jmethodID s_jni_method_alert;
@@ -677,9 +676,7 @@ JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_SetUserDirec
     JNIEnv* env, jobject obj, jstring jDirectory)
 {
   std::lock_guard<std::mutex> guard(s_host_identity_lock);
-  std::string directory = GetJString(env, jDirectory);
-  s_set_userpath = directory;
-  UICommon::SetUserDirectory(directory);
+  UICommon::SetUserDirectory(GetJString(env, jDirectory));
 }
 
 JNIEXPORT jstring JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_GetUserDirectory(JNIEnv* env,
@@ -778,7 +775,6 @@ JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_Run(JNIEnv*
   RegisterMsgAlertHandler(&MsgAlert);
 
   std::unique_lock<std::mutex> guard(s_host_identity_lock);
-  UICommon::SetUserDirectory(s_set_userpath);
   UICommon::Init();
 
   WiimoteReal::InitAdapterClass();