The main difference between waxed and unwaxed lemons is that waxed lemons have a longer shelf life. The waxing process of a citrus fruit, such as a lemon, can extend its shelf life by nearly 3 weeks if stored outside the refrigerator. If refrigerated, a waxed lemon will keep for a longer time.
An unwaxed lemon can have a shelf life of about a week if refrigerated. Unwaxed lemons are suitable for slicing, adding to a drink and as zest for a recipe. The waxed variety is an option if one requires its juice for cooking purposes. If someone has only waxed lemons and needs zest or peel for a recipe or dish, then it is necessary to scrub the lemons before using them.