Cupcakes filled with cream cheese, whipped cream or custard all require refrigeration to prevent these ingredients from spoiling. Although the sugar contained in a sweet cream-cheese filling helps to discourage the growth of bacteria, it's best to follow the U.S. Food and Drug Administration's "two-hour" rule when it comes to anything containing cream cheese. Never leave your cream cheese-filled cupcakes out of the refrigerator, set to 40 degrees Fahrenheit or below, for more than two hours. Discard any cupcakes that have been sitting out for longer than this time or for more than one hour in temperatures above 90 F to prevent foodborne illness.

When storing your filled cupcakes in the refrigerator, you'll need to wrap them first to keep them moist. Wrap frosted or unfrosted cupcakes in plastic wrap or aluminum foil. The cupcakes will keep for about one week, based on the shelf lives of both cake and cream cheese. Although you can wrap and freeze the cupcakes for around two months at 0 F, freezing will cause the cream cheese filling to become crumbly in texture and possibly affect its flavor. Instead, freeze unfilled cupcakes, wrapped in plastic or placed in freezer bags, then fill them after thawing them.

While refrigeration is necessary to prevent the growth of bacteria or other spoilage microorganisms in the cream cheese filling of your cupcakes, it can dry out the cake. To prevent this from happening, you can bake your cupcakes and store them in a cool, dark pantry for up to two days before filling, frosting and serving them. Cream cheese has a shelf life of up to two weeks, so you can make the filling well ahead of time and store it in a sealed container in your refrigerator to have on hand. When it's time to fill and frost the cupcakes, do so the day you plan to serve them to keep the refrigeration time to a minimum.

Use your senses to help determine whether or not your filled cupcakes are still edible. Cupcakes that smell strange or appear to have visible mold are definitely spoiled and should be discarded. Cut them open to check on the filling before eating them. If the filling smells sour, has an unusually grainy texture or appears discolored or watery, it's spoiled and you need to throw it away. Eating cupcakes with cream cheese filling that has spoiled can make you very sick. Note that cupcakes left out at temperatures between 41 and 135 F for longer than two hours may not smell or taste bad, but could contain bacteria and need to be thrown away.