Muffin storage tips from The Law Student's Wife: Issues with mushy muffins just a day or two after baking? As muffins age, rather than going stale, their moisture seeps to the outside, causing them to revert to a dough-like state. I've tried every method to reverse this soggy-muffin phenomenon, and all have failed. They key is prevention. Lay a few paper towels at the bottom of an airtight storage container. Place muffins inside, and lay a second paper towel on top. Store at room temperature. The paper towels will absorb the moisture, extending the shelf life of your muffins. Muffins also freeze fantastically. Wrap individually in plastic wrap, then place together in a lfreezer bag. Set desired number out the night before to enjoy in the A.M.