Learn How to Store Muffins the right way! Here’s everything you need to know about keeping your homemade muffins fresh for days, weeks, or months.

Muffins in a plastic container with a lid lined with paper towels.

To save time and money I’ll almost always make a double batch of healthy muffins, that way we can enjoy some fresh and store the rest for later because we all know they make the easiest breakfast or on-the-go snack!

But how long do muffins last? If stored correctly they’ll stay moist and flavorful for up to 3 months.

How to Store Muffins First 24 Hours

If you know the entire batch of muffins will be gobbled up in the first 24 hours, then storing muffins is easy.

Apple cinnamon muffins and pumpkin cream cheese muffins cooling off on a wire rack.

Bake and let them cool completely on a wire rack. Then all you’ll need to do is cover them with a clean kitchen towel, that’s it! They’ll keep fresh at room temperature without drying out, even overnight.

Recipe Tip

Pictured are apple cinnamon muffins and pumpkin cream cheese muffins (coming soon).

How to Store Muffins for Up to 4 Days

Here’s a quick overview of how to store muffins for up to 4 days. Want a hint? The secret is paper towel.

Muffins in a container lined with paper towels.
  • Cool: Let your muffins cool for 5-10 minutes in the pan, then transfer to a wire rack to finish cooling completely. Storing them when they have even a little bit of warmth will result in soggy muffins.
  • Line an airtight container: Grab a large plastic container and layer the bottom with paper towel, I find one large paper towel folded in half works great.
  • Add muffins: Place muffins on top the paper towel in a single layer, then add another layer of paper towel on top. Don’t skip the additional layer! This will help absorb moisture from all sides.
  • Store: Seal with airtight lid and store on a counter at room temperature for up to 4 days.

Why Do You Use Paper Towels?

The best way to store muffins is at room temperature, and paper towel is the key to peak freshness.

As muffins age, any moisture that forms will travel to the surface making them unpleasantly soggy. The paper towel acts like a sponge to soak up that moisture.

Another neat trick for removing moisture is using saltine crackers, just stick a few in the container.

Can I Store Muffins in the Fridge?

Most muffins no, because it alters their taste and texture. Regular whole grain muffins and banana muffins do well at room temperature.

However, some muffins are more wet than others like almond flour strawberry muffins and strawberry muffins.

Also many muffins made with almond flour, or any other nut flour, gluten free muffins have a lot of moisture. So do heavy on pumpkin puree muffins like healthy pumpkin muffins with cream cheese or any other heavy loaded fruit muffins like healthy apple muffins.

So I would say these types of muffins would benefit from refrigeration for 2 more days after initial 24 hour storage on a countertop. Then freeze after that.

Can I Freeze Muffins?

Yes! Here’s how to store muffins in the freezer and lock in flavor for up to 3 months. Also be sure to check out our full post how to freeze muffins for more tips and tricks.

Muffins in a Ziploc bag.

Storing in a Ziploc bag is the easiest method.

In a single layer, set your muffins inside and suck out as much air as possible to prevent freezer burn, I find using a straw helps. Seal the bag and set flat in the freezer.

You can also wrap each muffin in plastic wrap individually and then place in a bag.

How to Defrost Muffins

When you’re ready to enjoy a healthy treat grab a frozen muffin and let it thaw at room temperature.

Alternatively, place unwrapped muffin on paper towel and microwave, 20-30 seconds is perfect.

Top 7 Tips for Storing Muffins

  • Cool in a muffin tin for 5-10 minutes: That initial 5-10 minutes in the pan allows them to cool slightly and keep their structure, but any longer in the hot pan and you run the risk of overbaked, dry muffins.
  • Cool them completely: Make sure to cool muffins completely on a wire rack before storing in a container, the condensation will collect if they aren’t fully cooled.
  • First 24 hours: Most muffins keep well covered with a kitchen towel on the counter for the first day.
  • All muffins differ: Read your healthy muffin recipe carefully, some muffins need refrigeration after 24 hours or they get moldy fast.
  • Humidity where you live matters: By the ocean, at sea level is less dry for me. If you live in the mountains or prairies, it is more dry. Any moisture from the air can make your muffins soggy but storing them in an airtight container will help.
  • Replace paper towels: Check on the paper towels, if they get soggy after a day or two replace them for optimal freshness.
  • Summer vs. winter: In the summer it’s more hot and more humid in most places, therefore you might have to freeze muffins sooner. Keep an eye on your muffins and watch out for signs of mold.


How long do you have to leave muffins in the pan after baking?

Leave them in the pan for 5-10 minutes at the most, otherwise they will overbake.

How many days will muffins stay fresh?

Muffins will stay fresh for 3-4 days at room temperature, freeze after that to keep them fresh longer.

How do you refresh old muffins?

If muffins get a bit stale, sprinkle them with water, place in a brown bag, and bake in preheated oven set to 350 F for 30 seconds.

How do you store muffins so they don’t get sticky?

Let them cool completely so there is no moisture and condensation built up in the container.

Reader Favorite Muffin Recipes to Try

Easy Muffins for Beginners

Muffins in a plastic container with a lid.

How to Store Muffins

Here's everything you need to know how to store muffins fresh for days, weeks, or months the right way!
5 from 1 vote
Servings 12 muffins
Calories 11
Diet Vegetarian
Prep Time 5 minutes
Cooling Time 2 hours
Total Time 2 hours 5 minutes


  • 1-12 muffins


  • Bake muffins as per recipe and let them cool completely on a wire rack.
  • For the first 24 hours, just cover them with clean kitchen towel and store on a counter.
  • To store muffins for another 2-3 days, line large container with a lid with double folded paper towel. Place as many muffins on top as you can fit comfortably covering with another double folded paper towel sheet.
  • Place lid on top and store on a counter for 2-3 more days.
  • After transfer any leftover muffins into the freezer.


Reheat: Reheat muffins in a microwave in 15 seconds increments. Air fryer is also great for that!
Freeze: See our post on how to freeze muffins.


Serving: 1muffin | Calories: 11kcal | Carbohydrates: 2g | Protein: 0.4g | Fat: 0.1g | Saturated Fat: 0.01g | Sodium: 22mg | Fiber: 0.1g
Course: Muffins and Quick Bread
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

5 Secrets to Easy Healthy Dinners

Plus sign up for weekly emails with recipes to make your cooking stress free, delicious and healthy.

About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

Pin this recipe now to save it for later

Pin Recipe

You may also like

Leave a Reply

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

Recipe Rating

This site uses Akismet to reduce spam. Learn how your comment data is processed.