Shelf life of apples in muffins Some muffin recipes incorporate sliced apples inside muffins. My question is, will these apple slices become either rancid or old-tasting inside the muffin while being stored inside the refrigerator?
The long cooking and high heat from the oven will definitively kill most of the bacteria and inactivate some enzymes present in the apple such as the famous polyphenol oxidase
 responsible for the oxidation process that makes raw apples brown when sliced. 

However, this won't stop the apples (and of course the whole muffin) to spoil on the fridge over time. Moulded apple can be particularly bad because of patulin.