When preserving food, there are certain steps to take to be sure the food is safe after preserving. One of those steps is peeling produce. Why? Bottom line is food safety.
While the outside peels of many types of produce are nutritionally beneficial, those peels can hold onto microorganisms and dirt. Rinsing produce with water before peeling is the first step to remove microorganisms and dirt. Peeling physically removes that outer layer and drastically reduces contamination. After a final rinse with water, the food is ready to preserve.
Therefore, when a recipe says to peel the produce, it must be done. That recipe was developed and researched with that step included. Choosing to skip the peeling step can result in improperly processed food and spoilage.
Don’t let those peels go to waste! Save them to make a vegetable stock to freeze and use in soups and other recipes. Add them to your garden compost pile or feed your animals.
Source: National Center for Home Food Preservation