How to store muffins to keep them fresh?

You’ve just baked a large batch of bagels and you’re wondering how best to store them so they stay fresh and moist.

So how are muffins stored?

the short answer

After your rolls cool completely, place them in an airtight container or freezer bag and store on the counter for 3-4 days. If they are quite wet, consider lining the container or bag with paper towels to trap extra moisture.

Those are the basics that work for most bagels, but you may need to change things up a bit depending on your recipe and circumstances.

Interested in learning more? This is what we are going to discuss next:

  • if removing the muffins from the silicone or paper liners is so important
  • when should you refrigerate muffins
  • if necessary use paper towels

How to store muffins in a bag

How to store muffins in a bag

Let them cool before storing

Letting the rolls rest on a wire rack for half an hour allows them to release any extra moisture inside. So before you even think about transferring your freshly baked muffins to a bowl or bag, make sure they are completely cool.

If you skip that step, all that moisture will stay inside the muffins, gradually move to the surface, and you’ll end up with a soggy or soggy base. Nobody wants that to happen.

And if you don’t have a rack, just layer the muffins in a single layer on a plate making sure they’re not crowded. The results are almost the same.

Now, you may have read that you should strip your bagels of any paper or silicone coating you may be using. That is supposed to allow the baked goods to release steam and cool better.

The theory makes sense, but from my experience, following this advice doesn’t help much. There is still quite a bit of uncovered surface area that allows moisture to escape.

Of course, I’m not saying you shouldn’t remove the muffins from the liners after baking. I’m just pointing out that it might not change that much.

If you prefer to leave your muffins in their pans, I suggest you do a simple test. First, remove the liners from half of the muffins and leave the rest as is. Then compare how both types hold up after a day or two.

If one guy knows better than the other, you have a clear winner.

How to store muffins in a container
How to store muffins in a container. Note that I left them in linings.

How to keep muffins fresh and moist?

The best way to keep your rolls fresh and moist is to store them in a sealed airtight container or freezer bag. Make sure the muffins retain their moisture and don’t dry out too quickly.

The problem with small, sealed spaces is that whatever excess moisture is there has no way to escape. And if that moisture is inside your muffins, it’s going to move to the surface and collect there because it has nowhere to go. This is how you end up with soggy bagels after a couple days of storage.

The solution is to line the bowl with one or two paper towels and cover the muffins with another couple. Those paper towels will soak up that extra moisture leaving your bagels moist but not wet.

Related: How long do muffins last?

Does that mean you should always use paper towels when storing muffins? Not necessarily.

What I found is that only really moist buns tend to have soggy issues. I’m talking about those with a lot of fresh fruit and, therefore, water content. For those, paper towels should come in handy.

But for others, those paper towels probably won’t make much of a difference.

The bottom line is that if your muffins get soft after a couple of days in storage, make sure they cool completely and cover the pan with paper towels. Otherwise, don’t fix it if it ain’t broke.

muffins ready to store
muffins ready to store

Should I refrigerate muffins?

While many articles state that you should never refrigerate muffins, that’s not necessarily the case. Sure, most recipes store just fine on the counter for a couple of days, but in certain cases, refrigeration is definitely worth considering.

One such case is if you are using fresh, uncrushed fruit in your recipe. That means most blueberry, raspberry, and other fruit-based muffins out there.

I don’t know about you, but I wouldn’t feel comfortable leaving bagels topped with fresh fruit on the counter for more than a day or two. If you want to store them longer, you should refrigerate them.

And in case you’re wondering, I’m not the only person who recommends it. Kate from the Cookie & Kate blog recommends refrigerating her blueberry muffins if you need more than 2 days of storage.

In addition to muffins topped with fresh fruit, I also recommend refrigerating almost any type of savory muffin. That category includes biscuits with cheese (or other dairy), ham, sausage, and the like.

Now, let’s look at the last possible way to store muffins: the freezer.

freshly baked muffins
freshly baked cupcakes

Can you freeze muffins?

Most bagels freeze surprisingly well, and freezing them requires little time and effort. All you need is a couple of freezer bags or plastic containers and some spare space in the freezer.

To freeze your muffins, do the following:

  1. Let them cool down. If your kitchen still smells like freshly baked muffins, it’s probably too soon. Make sure those muffins are room temperature on the outside as well as the inside.
  2. Place them in containers or bags. If your rolls are moist on the outside or sticky, consider freezing them individually so they don’t stick together. For regular bagels, you can freeze as many as you like in a single bag or container. If you’re using a bag, squeeze out as much air as possible before sealing it.
  3. Throw everything in the freezer.

One thing worth noting is that if you expect the muffins to sit in the freezer for an extended period, like a month or more, it’s best to go with a bag. That’s because they don’t allow as much cold air around the buns as the containers do.


It’s best to freeze the rolls in a single layer so none of them get squashed. Also, if you’re afraid other food items might crush them, go with a container or put that bag in one.

How long can you freeze muffins, you ask? More than 3 months is a pretty safe bet and should be enough for most of us.

But if the muffins are staying in the freezer for a longer time, thaw them and assess the quality before serving. They are most likely pretty good.

Speaking of defrosting, leave your frozen bagels out on the counter until they come to room temperature. That can take anywhere from an hour to maybe three hours, depending on the size and what’s inside (the more moisture inside, the longer they’ll defrost).

Once your muffins thaw, be sure to eat them the same day.

Raspberry cupcakes dusted with powdered sugar
Raspberry cupcakes dusted with powdered sugar

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