If cupcakes only need to be stored for a few days, it is best to put them in an airtight container on the counter. To keep cupcakes fresh for longer than a few days, it is best to store them in a plastic bag in the freezer.
The refrigerator is not a good place to store cupcakes because this makes the cupcakes dry out and become stale more quickly. Unfrosted cupcakes can be stacked in one large freezer bag before going in the freezer. Frosted cupcakes are best stored in individual freezer bags. When ready to eat the frozen cupcakes, allow them to defrost on the counter for about two hours.