This post may contain affiliate links. Please read our disclosure policy.

Have you ever reached into a container of leftover muffins, eager for the fluffy bites of breakfast joy that await, only to discover that the outside of the muffins have become unpleasantly soggy? It’s a sad moment that, while it cannot be reversed, can be avoided with one simple trick. Here’s How to Store Muffins to prolong their shelf life and keep them fresh.

One simple trick will keep your homemade muffins fresh for longer. Here's how to store them (and keep them from getting soggy!) @wellplated

Before we delve in, let’s first address the issue at hand: Why do leftover muffins become soggy?

It is an odd phenomenon. Intuitively, you would think that, as muffins stale, the outsides would become dry. In reality, this just isn’t how muffin science (a delicious field I aspire to master) operates.

As muffins age, their moisture migrates to the surface. That moisture will try to evaporate and, if the muffins are wrapped in plastic or stored in an empty airtight bag or container, that moisture sinks right back onto the muffins’ surface. Unfortunately, there is no way to prevent this (aside from loading the muffins with preservatives), but we can delay the inevitable with a handy little tool I’m betting you have lurking in your kitchen right now.

Paper towels.

Let’s do this.

The Best Way to Store Muffins

STEP ONE: Let the muffins cool completely on a wire rack.

How to store muffins to keep them from getting soggy. @wellplated

Storing the muffins when they are even a little bit warm will result in even more condensation, as the muffins will still be letting off heat. Let them cool for no more than five-to-10 minutes in the pan, then transfer them to a wire rack to finish cooling completely.

STEP TWO: Line an airtight storage container with paper towels.

How to store muffins. This one simple trick will keep them from getting soggy! @wellplated

The paper towels will act like a “sponge,” absorbing the moisture the muffins emit as they age. Instead of sinking back into the muffin’s surface and making them soggy, the moisture will be absorbed by the paper towels. I like to use one large paper towel, folded in half to fit the container.

Alternatively, you can use a large ziptop bag, turned on its side so that it lays flat—just be sure you store the muffins in a single layer only (do not stack).

STEP THREE: Place muffins in the container, on top of the paper towels.

How to Store Muffins. The simple trick that keeps them fresh for longer. @wellplated

Or on the bottom of the ziptop bag, still atop the paper towels.

STEP FOUR: Place an additional paper towel layer on top of the muffins.

How to store muffins. One simple trick to keep them fresh! @wellplated

This is essential. You want to be sure to absorb moisture from all sides. Again, I use a large paper towel, folded in half.


How to store muffins so that they stay fresh and don't become soggy. @wellplated

Refrigerating the muffins will alter their flavor and texture. Room temperature is the way to go from maximum freshness.

STEP SIX: Enjoy!

This one trick will keep your muffins fresh for longer. No more soggy muffins! Here's how to store them the right way. @wellplated

The muffins will last two-to-four days stored this way (without this method, you’ll notice the “soggy” factor taking hold in fewer than 24 hours). If the paper towels become very damp, I recommend replacing them on Day 2 or Day 3.

For Storage Longer Than Four Days

  • To Freeze. I recommend freezing muffins that you’d like to keep beyond four days. Individually wrap them in plastic, then place them in a ziptop bag and freeze for up to 2 months.
  • To Reheat. Let thaw at room temperature or rewarm gently in the microwave.

My Favorite Muffin Recipes

I have DOZENS of Healthy Muffin Recipes for you to choose from, but here are a few ideas:

Did you try this recipe?

I want to see!

Follow @wellplated on Instagram, snap a photo, and tag it #wellplated. I love to know what you are making!

You May Also Like

Free Email Series
Sign Up for FREE Weekly Meal Plans
Each includes a grocery list, budget, and 5 healthy dinners, helping you save time, save money, and live better!

Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

Learn more about Erin

Leave a Comment

Did you make this recipe?

Don't forget to leave a review!

Your email address will not be published. Required fields are marked *


Leave a comment

  1. This advice is great and works for storing almost anything – a paper towel or a clean dish towel regulates the moisture in the box.

    This way of storing, in an airtight container with a towel, works for yeast bread, cakes and cookies (though you need to not mix these – bread, cakes and and cookies need different moisture levels and will make each other stale if kept together).

    You can even use this to prolong the life of fruit and veg in the fridge – take the produce out of its packaging and put it in a salad box lined with paper towels or clean dish towels, and it will stop condensation building up and causing rot. I find they will last about twice as long that way compared to being kept in their packaging in a bare box or shelf.

  2. If muffins have a consumable period of more than 5 days (indicated in the packaging), is it okay to not store it in a fridge within the period?

    1. May, these directions apply to homemade vs. packaged muffins (packaged muffins usually have preservatives or other added ingredients so that can stay fresh for longer). For packaged muffins, I’d follow whatever the packaging suggests.

  3. These came out perfect with a few minor substtutions goat milk yogurt, didnt have enough honey, so used part monk fruit.. used paper cubs that I sprayed lightly, but still hard to get out to much sticking to sides.. vety delicious , thank you so much for this recipe

  4. Hi. Good tips. I’ve used paper towels on top of baked goods when they are still warm and I need to take them to an event. Had not thought of placing the paper under though. Will definitely try. I have a question about muffins or bread with fresh fruit such as blueberries. Can you store them on the counter also?

  5. We always have fresh bread and muffins at our house- and this Christmas invested in a bread box. Our muffins last perfectly in it without the need for paper towels etc. Just another idea for anyone interested :) 

    1. Hi Mehwish! Are you referring to my Healthy Blueberry Muffins recipe? If so, yes, this method should work well!

Load More Comments