diff --git a/src/core/core.cpp b/src/core/core.cpp
index f313bd6cd..29a441c00 100644
--- a/src/core/core.cpp
+++ b/src/core/core.cpp
@@ -277,10 +277,11 @@ bool Core::InitializeBaseSettingsLayer(std::string settings_path, Error* error)
 bool Core::SaveBaseSettingsLayer(Error* error)
 {
   INISettingsInterface& si = s_locals.base_settings_interface;
-  if (si.IsDirty() && !si.Save(error, Settings::GetSectionSaveOrder()))
-    return false;
+  if (!si.IsDirty())
+    return true;
 
-  return true;
+  si.RemoveEmptySections();
+  return si.Save(error, Settings::GetSectionSaveOrder());
 }
 
 void Core::SetDefaultSettings(bool host, bool system, bool controller)