I mean, there are certain ingredients that are used in baked goods that extend shelf life.....like pastries with high fat and sugar content will last a lot longer than a loaf of french bread, which has no sugar or fat content. Generally, the more moisture a baked good can retain, the longer it will stay fresh.
In my 16 years of pastry work, I have used dough conditioners at times and emulsified shortenings, but I would not call these natural at all.
I honestly don't know if there is a "magic ingredient" you could add to a baked good and have it be completely all natural.