When you make cupcakes in advance of an event and have leftovers, proper storage keeps them fresh and moist. Storage methods vary, depending on whether you frost the cupcakes and the type of icing that you use. Cupcakes that are frosted or filled with dairy ingredients should not be stored at room temperature to prevent bacterial growth that causes food-borne illness. Always cool cupcakes completely before storing them to prevent the steam from making them soggy.
Counter Measures
If you're planning to serve the cupcakes within a short period of time after baking, and they’re not frosted with buttercream or filled with dairy ingredients such as whipped cream, cream cheese or ganache, you can keep them on the counter at room temperature for two to three days tops. Place the cupcakes in an airtight container and keep away from direct heat or sunlight. Keep the lid closed tightly so that the cupcakes don’t dry out. This storage method works well if you bake cupcakes a day or two before an event and frost them prior to serving.
Chill Out
Refrigeration extends the life of cupcakes and is necessary if you use dairy-based frosting and fillings. Seal the cupcakes in an airtight container before putting them in the refrigerator to keep them from drying out; paper cake boxes won't work because they don’t form an airtight seal. When properly stored in the refrigerator, unfrosted cupcakes can keep for up to one week; frosted and filled cupcakes are best eaten within two to four days.
Freezer Time
Unfrosted cupcakes -- wrapped in plastic and placed in resealable freezer bags -- can keep up to six months in the freezer. Frosted cupcakes should be treated a little more delicately. If you use bright-colored frosting, it might bleed when defrosted. Generally, it's a good idea to freeze a test batch of cupcakes to determine how your recipe reacts to the freezing process. The outcome of the test can help you decide how to handle freezing larger cupcake batches.
Life Happens
If something comes up while your baking cupcakes and you need to stop, freeze the cupcake batter and finish the project later. Cupcake batter can be frozen right in the cupcake liners, in freezer bags or in disposable muffin pans. You also could fill silicone cupcake molds with batter, freeze and then pop the frozen batter pucks into a freezer bag. When you’re ready for cupcakes, thaw the frozen baked ones or bake the frozen batter for an extra five to seven minutes.