These moist and tender gluten free pumpkin muffins are made with simple pumpkin puree, plenty of pumpkin pie spice, and a few chocolate chips (if you like). You can also leave out the chips entirely, or maybe replace them with chopped walnuts!

Oh, and did I mention that it only takes one bowl and just 30 minutes from start to finish for you to have yummy, pumpkin-y gluten free muffins in hand?

What makes these gluten free pumpkin muffins special

I love making pumpkin recipes with pumpkin butter, which is just pumpkin puree with added juice and warm pumpkin spices, cooked down to reduce moisture and intensify flavors. But this recipe is different.

To bake with pumpkin butter, you have to have made some or bought some, and it takes a bit of time to make. I usually have pumpkin butter in my refrigerator around this time of year, but it feels like a commodity.

Pumpkin butter also has added sugar, even if it’s unrefined pure maple syrup. And sugar is sugar.

This recipe for gluten free pumpkin muffins is made in one bowl, with no advance planning. They’re not particularly high in added sugar (3/4 cup in all 12 muffins), and they’re dense but tender and incredibly moist and flavorful:

  • Ease of preparation (30 minutes start to finish) and just one bowl
  • Intense pumpkin flavor (the right balance of ingredients + a bit more pumpkin pie spice)
  • Moist, tender, lightly sweet muffin that’s perfect for breakfast or a snack.
  • Freezes wonderfully so you can always have them on hand
Pumpkin chocolate chip muffin cut in half on small white plate

Tips for making these gluten free pumpkin chocolate chip muffins

While gluten free pumpkin muffins do take a bit of effort, they’re not difficult. Here are some of my top tips for making sure you get perfect gluten free muffins every time.

How to bake gluten free muffins with pumpkin puree

I can’t stop myself from baking with pumpkin, both from a can and from a whole roasted pumpkin (who doesn’t love toasted pumpkin seeds?!), but it can be tricky.

Pumpkin puree has quite a lot of moisture, and its pumpkin flavor is not really as intense as you might think. My usual solution is to begin by making a batch of homemade pumpkin butter, and this time of year I always have some in the refrigerator.

But I wanted the ease of simple gluten free pumpkin chocolate chip muffins that require no advance prep, and still have bright pumpkin flavor. (I am now giving thanks to my family for enduring batch after batch after batch of this and that pumpkin muffin during recipe testing.)

Using the right gluten free flour to nail this pumpkin muffin recipe

There are lots of gluten free flour options out there, including single-ingredient gluten free flour, like oat flour, coconut flour, and almond flour.

While I firmly believe that each of these has its place in gluten free recipes, it’s not in this recipe.

For these pumpkin muffins, I used Better Batter’s classic blend gluten free, and that’s what I recommend you do, too. It took a lot of experimenting to find the right ratio of dry and wet ingredients to get these muffins just right, and Better Batter gluten free flour got me there.

If you use a different all purpose gf flour, you might see okay results, but they may also turn out very differently than the yummy ones I achieved. You can always use Cup4Cup as well, and you’ll get slightly more cakelike muffins, but the recipe will still work.

But I don’t recommend trying to come up with your own gluten free flour blend for this one, as you’ll struggle to get consistent results.

Room temperature ingredients are a must for better results

Using room temperature ingredients is a good idea for all types of gluten free recipes, but I think it’s extra important here, especially if you’re using leftover pumpkin puree for this recipe.

Throwing in cold puree (or milk or butter) will make it more difficult for you to mix your batter. It will also cause other ingredients that are meant to be at room temperature, like butter, to clump and refuse to blend.

Quick and Easy Gluten Free Pumpkin Chocolate Chip Muffins, Step by Step

How to store gluten free pumpkin chocolate chip muffins

One of my favorite things about these gluten free pumpkin chocolate chip muffins is their grab-and-go convenience. They’re perfect for a quick breakfast, a hearty snack, or healthy dessert.

So when it comes to storage, I’m so happy to report that you can keep them on the counter, in an airtight container, for 2 to 3 days. They rarely last that long in my house, but they do stay moist and tender for several days.

Can I freeze gluten free pumpkin chocolate chip muffins?

These gluten free muffins also freeze well, again making them awesome for convenient snacking. I like to wrap each in cling wrap before putting inside a freezer-safe bag. If you want a delicious muffin in the morning, just take one out the night before and let it defrost on the counter.

Can’t wait that long? You can also defrost them in the microwave. Just give each 20-second blasts until they’re soft.

Pumpkin chocolate chip muffins baked in muffin tin

Gluten free pumpkin chocolate chip muffins: ingredients, substitutions, and variations

Like most gluten free pumpkin recipes, you can tweak these pumpkin muffins to suit your own dietary requirements and taste preferences with just a little imagination and know-how. Try these variations if you suffer from food allergies like an egg allergy, food sensitivities, or need to follow an additional special diet.

Gluten free dairy free pumpkin muffins

In place of the butter, I recommend trying vegan butter. My favorite brands of dairy free butter are Melt and Miyoko’s Kitchen. I don’t recommend using Earth Balance buttery sticks, as they have too much moisture and may cause the muffins to rise and then sink. I dont recommend coconut oil here, either. Coconut oil behaves differently than butter when baking.

In place of buttermilk, use half plain nondairy yogurt by volume and half nondairy milk by volume. You can also use those proportions if you can have dairy, but don’t have buttermilk. It works really well.

If you’re dairy-free, make sure your chocolate chips are dairy-free, too.

Gluten free egg free pumpkin muffins

There are two eggs in this recipe, and that is usually the upper limit for replacing eggs with one “chia egg” each.

For each “chia egg,” place 1 tablespoon of ground white chia seeds and 1 tablespoon lukewarm water in a small bowl, mix, and allow to gel.

Gluten free, vegan pumpkin muffins

To make vegan and gluten free pumpkin muffins, just follow my suggestions above for replacing the dairy and egg and make sure that your sugars aren’t made with bone char.

Gluten free, sugar free pumpkin muffins

While I haven’t tried it myself, I imagine that you can swap out the sugar in this recipe for a granulated sugar alternative of your choosing. Just make sure it’s granulated and not liquid so as not to upset the ratios in this gluten free pumpkin muffin recipe.

Coconut sugar is a popular option for those who want to avoid heavily refined white sugar. Coconut sugar comes from the coconut palm and can be used a a one-for-one substitute for regular white or brown sugar. Note that it tastes more like brown sugar than white, as it has an almost caramel-like flavor. You could also use fructose or date sugar for healthier, less refined sugar options.

And, for sugar-free baking, you could try allulose, Swerve, or granulated inulin.

Gluten free pumpkin muffins with applesauce

I know that applesauce is a popular alternative to butter, eggs, and sugar, but I don’t recommend it for this recipe. Remember, you have to have the right balance of moisture to make these gluten free pumpkin muffins work, and I worry that using applesauce in place of these ingredients will just make the batter too wet.

How to use canned or fresh pumpkin puree in these gf pumpkin muffins

This recipe is created to be made with canned, single-ingredient pumpkin puree, not pumpkin butter, which is a more concentrated version that is cooked down with sweetener and spices. The extra moisture that pumpkin puree has, compared to pumpkin butter, is needed here.

If you would like to make your own pumpkin puree using a fresh pumpkin, you can click through in the link above and follow the instructions there—but stop short of making pumpkin butter.

Since much canned pumpkin puree is actually made from other types of squash, not actual pumpkins, you can try using another type of squash. Your muffins may end up being less orange in color, and taste a bit different, but the recipe would still work.

Gluten free pumpkin muffin variations

I don’t know about you, but it’s not often that I’m looking for ways to leave chocolate out of my life. However, there are times when I’m craving something a little different, so I do have variation ideas for these yummy gluten free muffins.

Instead of chocolate chips, try half a cup of chopped walnuts or pecans. Both harmonize with the pumpkin flavor so wonderfully.

You can also try raisins in place of chocolate or in addition to the nuts if you’re going dairy free or want a different type of sweetness.

You could up your spice game, too, by adding just a hint of chili to alongside the pumpkin spice mix.

A close up of the inside of a pumpkin chocolate chip muffin on a white plate


Are these pumpkin chocolate muffins healthy?

These pumpkin chocolate muffins are relatively healthy. They don’t have a ton of sugar, and they offer all the dietary benefits of consuming pumpkin, including lots of antioxidants, minerals, and vitamins.

If you want to make them even healthier, you can skip the chocolate or exchange it for mixed nuts.

Can I use this recipe to make mini pumpkin chocolate chip muffins?

You can definitely use this recipe to make pumpkin chocolate chip mini muffins rather than full-sized ones. The only thing that will need adjusting is the cook time.

I would suggest checking the mini muffins starting at 10 minutes and using the toothpick test to judge whether they’re done.

How do you know when gluten free pumpkin chocolate chip muffins are done?

Because oven operating temperatures can vary widely, I recommend that you use the toothpick test to determine if your gf muffins are ready. Be sure to use a light-colored muffin tin, though, or they’ll burn on the outside before the inside has finished baking entirely.

At about the 20-minute mark for regular-sized muffins, insert a toothpick and pull if out. If it comes out with gooey batter, continue cooking. If it comes out with just a few crumbs, your pumpkin muffins are ready.

What the best gluten free flour blend for this pumpkin muffin recipe?

For these gluten free pumpkin muffins, I recommend that you use Better Batter. It’s the flour blend I used when perfecting this recipe, and the only one I suggest if you want to duplicate my results as closely as possible.

Why are my gluten free pumpkin muffins so dense?

Dense gf muffins are typically the result of too much moisture, or leaveners that aren’t fresh. If yours came out heavy, double-check what you’re adding to your recipe, and check the use-by date on your baking powder and baking soda. If you made your own puree, drain off some of the water before blending for your next batch.

Why did my gluten free pumpkin chocolate chip muffins come out gummy?

If your gluten free pumpkin muffins come out gummy, it’s probably because your gluten free flour mix wasn’t one of my recommended blends, or you overmeasured some of the liquid in the recipe.

This can also happen if you go off-recipe and use a different type of gf flour, like almond flour or oat flour. It could be that these flours absorb too much moisture or require a different ingredient ratio to work out just right.

Finally, your muffins may be gummy if your oven isn’t at the right baking temperature. If the temperature is too low, they may not rise properly. If it’s way too high, the outside will become dark before the inside has the right baked structure.



Gluten Free Pumpkin Muffins | Quick and Easy, with chocolate chips

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Fill your home with the scents of fall when you bake these gluten free pumpkin muffins with chocolate chips. Whip up these gluten free chocolate chip pumpkin muffins in just 30 minutes.
Course Breakfast, Muffins
Cuisine American
Keyword gluten free pumpkin muffins
Prep Time 10 minutes
Cook Time 20 minutes
Servings 12 muffins
Author Nicole Hunn


  • 2 cups all purpose gluten free flour blend (I used Better Batter; please click thru for more info on appropriate blends)
  • 1 teaspoon xanthan gum omit if your blend already contains it
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon kosher salt
  • 2 teaspoons pumpkin pie spice
  • ¾ cup granulated sugar
  • 6 tablespoons unsalted butter at room temperature
  • cup pure canned pumpkin puree at room temperature
  • 2 eggs at room temperature, beaten
  • ¼ cup buttermilk at room temperature
  • 4 ounces semisweet chocolate chips optional


  • Preheat your oven to 350°F. Grease or line the wells of a standard 12-cup muffin tin and set it aside.
  • In a large bowl, place the flour, xanthan gum, baking powder, baking soda, salt, pumpkin pie spice, and granulated sugar, and whisk to combine well.
  • Create a well in the center of the dry ingredients in the large bowl and add the butter, pumpkin puree, eggs, and buttermilk, mixing to until just combined after each addition. The batter will be thick but soft.
  • Add all but about 1 tablespoon of the (optional) chocolate chips to the batter, and mix until just evenly distributed throughout.
  • Divide the batter among the prepared wells of the muffin tin and sprinkle the remaining few (optional) chips evenly over the tops of the batter in each well, pressing gently to help them adhere.
  • Shake the pan back and forth to distribute the batter evenly in each well of the muffin tin. Place the muffins in the center of the preheated oven.
  • Bake the muffins in the tin until a toothpick inserted in the center of a muffin comes out with no more than a few moist crumbs attached (about 20 minutes).
  • Remove the pan from the oven. Allow the muffins to cool in the tin for 5 minutes before transferring to a wire rack to cool completely.



Originally published on the blog in 2015. In 2020, video, some photos, and most text new; recipe mostly unchanged. In 2022, more text resources added.
A small pumpkin chocolate chip muffin on a white plate
Pumpkin Chocolate Chip Muffin whole and mufin cut in half

The post Gluten Free Pumpkin Muffins | quick & easy with chocolate chips appeared first on Gluten Free on a Shoestring.

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