How to Store and Freeze Muffins

5 from 58 votes

Knowing how to store and freeze muffins is something every home baker and muffin-lover needs to know! Learn my tips for keeping your muffins free from sogginess, how to store them in the fridge or freezer to enjoy later, and how to dethaw them!

muffins in a tupperware on paper towels next to a cooling rack, which is one way how to Store and Freeze Muffins

You did it! You made muffins! 

I have to know… Did you make blueberry muffins or strawberry muffins? Or perhaps pumpkin muffins or maybe banana muffins

Honestly, you can’t go wrong with the kind of muffins you make. However, even though muffins are a great make-ahead breakfast, storing them can be tricky.

If you’ve ever reached for a leftover muffin only to discover it too dry or too soggy, then you’re going to want to know my tricks for storing muffins the right way. 

I’m something of a muffin expert, but trust me when I say I learned these lessons the hard way.

The best way to store muffins depends on how soon you want to eat them: 

  • Within 3 days of baking them: Store them on the countertop at room temperature. 
  • In the next few days: Store them in the fridge, but with the risk of a change in texture. Alternatively, store what you’ll eat in the next few days using the countertop method, then freeze the rest. 
  • Within the next 3 months: Store them in the freezer — reheat when you get a muffin craving! 
healthy no sugar added blueberry muffins in a silver muffin tin on a white marble countertop

I’m going to show you how to store homemade muffins on the counter, in the fridge and in the freezer, but they all start with the same first step: 

How to keep muffins fresh, no matter how you store them

If you’re baking your muffins, the first thing you need to do is let your muffins cool down all the way. I get it. You’re ready to clean up your counters and put those puppies away, but try to resist the urge. 

Why? If you store them too soon, any residual heat will turn to condensation. The condensation is water that gets trapped in your storage container with nowhere to go... except drip onto your muffins and make them soggy. It’s even worse if you have a fruity recipe, such as blueberry muffins.

There is nothing worse than a soggy muffin, so here’s how to handle this: 

  1. First, let them cool in the muffin pan for a few minutes. 
  2. Then transfer them to a wire rack to cool more. 
  3. When the muffins are fully cooled down, after at least an hour, it’s safe to store them. 

It doesn’t matter if you use paper muffin cups or silicone ones — they will still need lots of time to cool down fully. 

On the flip side, if you leave them out too long they can get stale and dry. So it’s imperative to time this out perfectly. (It’s not hard though, I promise.) 

Healthy banana chocolate chip yogurt muffins in white paper muffin cups on  a silver wire cooling rack

How to store muffins on the counter at room temp

Room temperature muffins are the ideal texture. The best way to store them is in a resealable, food-safe storage container. Glass or plastic is fine. 

This method is perfect for storing muffins overnight, especially if you bake them today and want to serve them tomorrow morning. 

I have a trick for keeping your muffins moisture-free: 

  1. You’ll want to place a paper towel in the bottom of your storage container or ziptop bag. This will give any remaining moisture a place to land. 
  2. Then place cooled muffins on top in one layer. Don’t stack them. 
  3. Before adding the lid, place another paper towel on top. This helps the muffins from getting too moist and spoiling. 
  4. Change out paper towels if they become moist. 

Feel free to use a folded kitchen towel in the bottom of your container instead if you want to avoid waste. 

How long do muffins keep at room temp? 

If stored at room temperature on the counter, you should eat the muffins within 2-3 days. If they aren’t going to be eaten within that time, I recommend refrigerating or freezing them instead.

muffins in a sealed tupperware with paper towels that are ready to be stored -- learn how to Store and Freeze Muffins

How to store muffins in the fridge 

For storing muffins in the fridge, use that same paper towel method. 

Be warned: Refrigerating muffins can add back some of the moisture and it can change the texture of the muffins. 

But it will also help your muffins to last a few more days than they would on the counter. The paper towels will help trap any extra moisture. 

If your muffins have fresh fruit, such as blueberry muffins or apple muffins, you may want to do the fridge option to avoid a chance of mold. 

You may want to microwave them for 10-15 seconds to reheat them or warm them in the oven. 

How long do muffins keep in the fridge? 

Refrigerated muffins should last 4-5 days. If you don’t plan to eat them all in that time, you may want to freeze some of them. 

blueberry muffins on a cooling rack next to a tupperware

How to store muffins in the freezer 

Freezing muffins is the best way to enjoy muffins for a while after you make them. 

There are two ways to store muffins in the freezer. The first way is to individually wrap the muffins so they don’t stick together, and it also helps prevent freezer burn.

Learn my two favorite methods for how to store and freeze muffins:

How to wrap muffins for freezing

  1. Once the muffins are totally cooled, wrap them individually with plastic wrap
  2. Then store them in a ziptop freezer bag or resealable food storage container. 

The second way is my favorite method, called quick freezing. Quick freezing helps to ensure that the muffins don’t stick together in the bag so that you can more easily pull them out of the container individually. 

How to quick-freeze muffins

  1. Place the muffins in the freezer on a baking sheet or your cooling rack for 15 minutes. 
  2. Then you can move them to a container or freezer-safe bag, and place them back in the freezer. 

I currently have a stash of a few flavors of frozen muffins in my fridge, including coffee cake muffins and breakfast frittata muffins. (Even though they’re not a traditional breakfast muffin, you can follow the same steps to store egg muffins in the fridge or freezer.) 

How long do muffins keep in the freezer?  

Frozen muffins will last 2-3 months in the fridge. 

How to thaw and reheat frozen muffins 

There are a few ways you can thaw and reheat frozen muffins. 

  • Thaw at room temperature: Set them out on the counter the night before you plan to eat them. 
  • In the oven: Reheat in a 350°F oven for 10-15 minutes to thaw and warm up. 
  • In the microwave: Remove from plastic wrap and place on a microwave-safe plate. Warm a frozen muffin in the microwave for 30 seconds. If not fully warmed, keep heating in 30-second increments (can vary depending on the size of the muffin). 
8 blueberry muffins on a white cake stand, with a bite taken out of one

How to store store-bought muffins

Okay, so you didn’t make your muffins. As much as I love baking, I don’t blame you one bit — I am definitely guilty of indulging in Costco muffins from time to time. 

But they are so big, so it's very helpful to know how to store and freeze muffins you buy from a bakery.

Since they are already baked and likely cooled down, you can skip right to the storage and freezing steps. 

Do not keep them in the same container they come in, as those plastic clamshells are not as airtight and trustworthy as a ziptop bag or a plastic storage container. (Glass containers also work.)  

Instead, use the paper towel method to keep the muffins fresh. 

Storing other kinds of muffins 

You can also use these methods for storing other baked goods, both sweet and savory, such as English muffins, scones, quick breads or cornbread muffins. They even work for storing gluten-free muffins and mini muffins!

Now that you know how to store and freeze muffins for the long haul, it’s time for you to get to baking! What kind of muffins will you freeze?  

muffins in a sealed tupperware with paper towels
Print
5 from 58 votes

How to Store and Freeze Muffins

Learn how to store and freeze muffins to keep them fresh!
Prep Time5 minutes
Active Time5 minutes
Inactive Time1 hour
Total Time1 hour 10 minutes
Course: Muffins
Keyword: bakery muffins, egg muffins, english muffins, gluten free muffins, how to freeze muffins, how to refrigerate muffins, how to reheat frozen muffins, how to store muffins, how to store muffins at room temperature, how to thaw frozen muffins, muffins, scones
Yield: 12 muffins
Author: Madison | A Joyfully Mad Kitchen
Cost: $10

Equipment

  • oven mitts
  • cooling rack

Materials

  • muffins
  • large plastic or glass food storage container or gallon-size ziptop freezer bags
  • paper towels
  • plastic wrap

Instructions

  • Cool the muffins
  • If using store-bought muffins, skip to the next section.
  • Remove muffins from the oven according to recipe instructions. Let cool for 10 minutes.
  • Place on a wire rack and let cool completely, at least 1 hour.
  • How to store at room temperature
  • Line a tupperware or gallon ziptop bag with 2 paper towels. Place muffins in a single layer on top. Add two more paper towels on top.
  • Leave on the counter or in another room-temperature area. Enjoy within 2-3 days.
  • How to store in the fridge
  • Line a tupperware or gallon ziptop bag with 2 paper towels. Place muffins in a single layer on top. Add two more paper towels on top.
  • Place in the fridge. Enjoy within 4-5 days.
  • How to store in the freezer with the quick freeze method
  • Place the muffins in the freezer on a baking sheet or your cooling rack for 15 minutes.
  • Move them to a container or bag.
  • Place them back in the freezer. Thaw before eating. Enjoy within 3 months.
  • How to store in the freezer with the individually-wrapped method
  • Once the muffins are totally cooled, wrap them individually with plastic wrap
  • Then store them in a ziptop freezer bag or resealable food storage container.
  • Place them in the freezer. Thaw before eating. Enjoy within 3 months.
  • Thaw and reheat frozen muffins 
  • Thaw at room temperature: Set them out on the counter the night before you plan to eat them. 
  • In the oven: Reheat in a 350°F oven for 10-15 minutes to thaw and warm up. 
  • In the microwave: Remove from plastic wrap and place on a microwave-safe plate. Warm a frozen muffin in the microwave for 1 minute. If not fully warmed, keep heating in 30-second increments. 
5 from 58 votes (58 ratings without comment)

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