diff --git a/Source/Android/jni/NativeConfig.cpp b/Source/Android/jni/NativeConfig.cpp
index 14d7d4af3e..270a999d0c 100644
--- a/Source/Android/jni/NativeConfig.cpp
+++ b/Source/Android/jni/NativeConfig.cpp
@@ -128,7 +128,12 @@ Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_unloadGameIn
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_save(
     JNIEnv*, jclass, jint layer)
 {
-  return GetLayer(layer, {})->Save();
+  const std::shared_ptr<Config::Layer> layer_ptr = GetLayer(layer, {});
+
+  // Workaround for the Settings class carrying around a legacy map of settings it always saves
+  layer_ptr->MarkAsDirty();
+
+  return layer_ptr->Save();
 }
 
 JNIEXPORT jboolean JNICALL
diff --git a/Source/Core/Common/Config/Layer.h b/Source/Core/Common/Config/Layer.h
index cbfbbe6aae..5c4185cdfe 100644
--- a/Source/Core/Common/Config/Layer.h
+++ b/Source/Core/Common/Config/Layer.h
@@ -138,6 +138,8 @@ public:
     m_map.insert_or_assign(location, std::move(new_value));
   }
 
+  void MarkAsDirty() { m_is_dirty = true; }
+
   Section GetSection(System system, const std::string& section);
   ConstSection GetSection(System system, const std::string& section) const;