Muffins come together handily for a satisfying snack, but their texture can change undesirably when you store them. Naturally moist muffins tend to get sticky and soggy in lidded containers and zip-top bags that prevent air circulation. To keep them fresh but not mushy, you must manage the moisture when you store them. Preventing soggy muffins starts with following the recipe carefully and cooking them fully before you take them out of the oven.
Check for golden brown edges and firm domed tops that spring back slightly when you touch them before you take the muffins out of the oven. Insert a toothpick directly into the center of a muffin; it should come out either dry or with just a few moist crumbs attached. If you see batter on the toothpick, return the muffins to the oven and repeat the toothpick test every 2 minutes until the muffins are done.
Cool the muffins in the baking tin for several minutes. Remove them from the cups and cool them completely, for about an hour, on a wire rack.
Put a paper towel in the bottom of a large airtight container. Place the muffins in a single layer in the container, and top the layer of muffins with another paper towel before putting the lid on the container. Eat them within a few days. To keep muffins long-term, wrap them individually in aluminum foil, place them in an airtight container and store them in the freezer for up to a month.
Reheat individually wrapped frozen muffins in the oven rather than the microwave. Preheat the oven to 300 degrees Fahrenheit and place foil-wrapped, frozen muffins in the oven, directly on the baking rack. Bake for 12 to 18 minutes, unwrapping to check for even heating. Reheat several muffins at once to make the process more efficient. If the muffins seem soggy after baking, unwrap them and turn on the broiler for a minute or two before taking them out.
Throw out muffins that become slimy, grow mold or develop an "off" smell during storage.