diff --git a/Source/Android/jni/MainAndroid.cpp b/Source/Android/jni/MainAndroid.cpp
index 4c7345b8dd..3dfafacf7c 100644
--- a/Source/Android/jni/MainAndroid.cpp
+++ b/Source/Android/jni/MainAndroid.cpp
@@ -74,6 +74,7 @@ IniFile s_ini;
 // sequentially for access.
 std::mutex s_host_identity_lock;
 Common::Event s_update_main_frame_event;
+Common::Event s_emulation_end_event;
 bool s_have_wm_user_stop = false;
 }  // Anonymous namespace
 
@@ -282,9 +283,17 @@ JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_PauseEmulati
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_StopEmulation(JNIEnv* env,
                                                                                   jobject obj)
 {
-  std::lock_guard<std::mutex> guard(s_host_identity_lock);
-  Core::Stop();
-  s_update_main_frame_event.Set();  // Kick the waiting event
+  {
+    std::lock_guard<std::mutex> guard(s_host_identity_lock);
+    s_emulation_end_event.Reset();
+    Core::Stop();
+
+    // Kick the waiting event
+    s_update_main_frame_event.Set();
+  }
+
+  // Wait for shutdown, to avoid accessing the config at the same time as the shutdown code
+  s_emulation_end_event.Wait();
 }
 
 JNIEXPORT void JNICALL
@@ -598,6 +607,8 @@ static void Run(JNIEnv* env, const std::vector<std::string>& paths,
     ANativeWindow_release(s_surf);
     s_surf = nullptr;
   }
+
+  s_emulation_end_event.Set();
 }
 
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_Run___3Ljava_lang_String_2(