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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:

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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

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  1. You have such great ideas! Thanks, and I’m not a student husbands wife or anything, great tips great recipes, and as for ” moist”, there really isn’t a suitible synonym for it, I’m from Florida, how about “humid” or I love “irriguous” or saturated,

    1. Humid? Lol. That is just hilarious. You are right–the “m” word is pretty much the only one that does the job. So glad you found this tip helpful Diana! Thanks for your comment and happy that you found my blog. Have a great day!

  2. Hi – I have found that keeping muffins in a perforated veggie bag on the counter works great for several days. I will keep about 6 in the veggie bag and freeze the other 6. I don’t even nuke the frozen ones – they only take a few minutes to thaw all on their own….

  3. Such a helpful post, thank you so much Erin!! I have a hard time letting baked goods cool completely because I have zero self control…;)

    1. Same here Marina! I find I just keep picking “one more bite” while they cool. Less muffins to store that way ;-)

  4. FANTASTIC tip, Erin! It’s a total bummer when you get SO excited about waking up to one of the muffins you baked the morning before, only to find that they are a soggy mess. But problem solved! Hooray! 

  5. We just put them all in a large tupperware and freeze them after they’ve cooled, without pre wrapping them or anything. about 40 seconds in the microwave and they are warm and fluffy again. I think it’s somewhat more ecological than individually wrapping – at least we’ve never had any problems with it.

    1. Ana, I love your ecological suggestion! I usually freeze mine (after they are *completely* cooled) by the dozen in a container or large ziplock bag (which I reuse!) – muffins thaw perfectly through the day in small single-serve containers that I pop in my lunch bag. :) 

  6. Thanks for the tip! I’ve been plagued for years by the dreaded second day soggy muffin! I will definitely try this!

  7. Thank you Erin, I knew there must be a way to do that …..good to know……you are so smart….why didn’t I think of that ? :) 
    I figured a way to keep cheese longer, but hadn’t figured out the muffins …..mine always gets a little gooey on top……but I always keep them in fridge too…. guess it’s best to just freeze them eh , and just take them out as you want one ? 

    1. I definitely find that refrigerating alters their texture. Since muffins are so quick to thaw, when in doubt, I say freeze!

  8. This is so fantastic, thanks so much for sharing. I always end up having to throughout my muffins — but not any more! :)

  9. Love this post! Sometimes I forget to do this genius little trick and it’s the pits when the muffins are blech. I need to print this post and hang it on my refrigerator. :)

  10. I need a wire rack – I can’t believe I’ve lived for so long without one in my kitchen. Thanks for another reason to buy one!

  11. Thank you soooooooooo much for the awesome trick.  I  love to cook and  bake.  I  always make too much,  our kids are all grown and have started their lives, but I still make too much for my husband and I.  This will  cut down on wasting things that I love to cook, bake,and of course EAT! Thanks again sweetie!

    1. Jody, I am so happy to hear that this post is helpful for you! I also hate wasting things, and with there only being two of us, I’m constantly looking for ways to prolong shelf life. I hope it’s equally helpful for you too!

    2. Jody, I am so happy to hear that this post is helpful for you! I also hate wasting things, and with there only being two of us, I’m constantly looking for ways to prolong shelf life. I hope you and your hubby enjoy many a fresh muffin :)

  12. Thanks for this suggestion. Just wondering – is there any difference if the muffins are baked in paper cups? I typically use these as I normally are baking muffins to take somewhere else (couldn’t keep them in my house and eat them all!) Thank you!

    1. Hi Susan! I don’t usually use paper cups, so I haven’t specifically compared the two, but I think that the process would be the same. I hope that it is helpful!

    1. Hi Rose, I’m not familiar with oxygen absorbers, so afraid this is out of my realm of expertise. It sounds like an interesting idea though!

  13. what about storage for muffins made with yogurt? I recently tried out a new banana yogurt muffin recipe that I love but I have no idea best storage for it! is it necessary to keep them in the fridge?

  14. 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.

  15. 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.

  16. 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

  17. 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?

  18. 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!