The apple muffins can be stored in an airtight container at room temperature on the countertop for up to 4 days. Make sure to cool them completely first. Then line the bottom of the container with a paper towel and store the muffins in a single layer. They can be refrigerated for up to 6 days. They can also be frozen in a freezer bag for up to 3 months. To reheat frozen muffins, let them thaw at room temperature or pop them in the microwave for a minute.