This is a personal choice and this recipe can be made with or without the peels. There are a few things to keep in mind when you are deciding if you want to peel your apples or not: - Apples, like a lot of fruit, are often sprayed for pests a few times during the growing season. Little critters are attracted to the sweetness of fruit! Any spray would sit on the outside of the apple on the peel. This could be true for organic or conventionally grown apples, but the type of pest control would be different in each case. - Apples are often coated in a food-safe wax for freshness. If you've even noticed that apples in the grocery store are shiny and apples sold direct from a farm look a little more dull, wax could be the reason. - If you opt to leave peels on, give your apples a good wash before using them.