Safety First

• Cream cheese is a highly perishable dairy product, and cupcakes filled with it should be refrigerated at 40 degrees Fahrenheit or cooler. You should even store cupcakes frosted with cream cheese frosting in the refrigerator. After baking, allow the cupcakes to cool completely before you fill or frost them. Place the cupcakes in a covered plastic container or on a baking dish and cover them with plastic wrap. Ensure the plastic wrap doesn't touch the frosting, which can smear it. Another option is to put the cupcakes in the refrigerator unwrapped for 15 minutes to harden the frosting before wrapping them.

Shelf Life

• If you're serving cream cheese-filled cupcakes immediately, you don't need to refrigerate them. If not, you should put them into the refrigerator within 2 hours of filling them, according to the U.S. Department of Agriculture. Stored this way, they'll safely last for three to five days.

Best Taste

• Although cupcakes filled with cream cheese should be stored in the refrigerator, they'll taste best if you let them come to room temperature before you serve them. Take the cupcakes out of the refrigerator 30 minutes to an hour before you plan to serve them. This takes the chill off the cake so it tastes moist and flavorful.

Deep Freeze

• Although cupcakes can safely be stored in the freezer before you fill them, once you fill them, you should keep them in the refrigerator instead. Cream cheese tends to become watery after it's been frozen, which can lead to disappointing results. To freeze unfilled cupcakes, wrap them tightly in plastic wrap or place them in large plastic freezer bags. Seal them and freeze them for up to three months. Thaw them at room temperature before filling and frosting them.