Gluten Free Pumpkin Muffins
These gluten free pumpkin muffins are the perfect Fall recipe. They’re filled with chocolate chips and topped with cinnamon streusel. They’re light, fluffy and so easy to make!

It’s officially pumpkin season and I for one am so excited. Pumpkin bread, pumpkin cookies, pumpkin pie and these new gluten free pumpkin muffins!
I couldn’t decide between doing chocolate chips or a cinnamon streusel topping, so I opted for both! These muffins have a generous amount of pumpkin for a very soft and tender texture, plus plenty of spice for tons of flavor. They’re perfect for a quick snack or dessert and I promise you’d never tell they’re both gluten and dairy free.
These muffins are made with gluten free all purpose flour and good old sugar, but if you’re looking for a healthy muffin recipe with almond flour, try my sweet potato muffins instead! If you’re really in the Fall baking spirit, my gluten free pumpkin cinnamon rolls and gluten free pumpkin pie always hit the spot.
Tips before we get started!
- I love these with both the streusel and chocolate chips, but you can opt to do just one or keep the muffins plain! The base recipe has tons of flavor as is.
- Be sure to use pure pumpkin puree, not pumpkin pie filling.
- For extra tall muffins, you can bake in two muffin tins and just bake 6 at a time, leaving space between each muffin. This allows the air to circulate better and creates taller muffins.

How to make gluten free pumpkin muffins
WHISK WET. In a large mixing bowl, whisk together all wet ingredients until smooth.
WHISK DRY. Whisk in the dry ingredients, making sure to spoon and level the flour. Fold in the chocolate chips. Scoop the batter into a muffin tray, filling each to the top to ensure nice round muffin tops.
MAKE STREUSEL. In a small dish, combine the sugar, flour and pumpkin pie spice. Cut in the butter or coconut oil with a fork until crumbly.
BAKE. Use your fingers to sprinkle the streusel on top of the muffins. Bake for 28-32 minutes or until a toothpick comes out clean.
SERVE. Let cool for about 15 minutes in the tray, then remove and transfer to a wire rack to finish cooling and enjoy!

WANT TO SAVE THIS RECIPE?
Can I make them vegan?
You can try subbing the eggs for an egg substitute like flax eggs or a store bought egg replacer, but they likely won’t rise as well. The eggs are important here for a fluffy texture and ensuring a nice rise, so I recommend sticking with the recipe as written for best results!
Vegan and gluten free baking is very tricky, so it’s usually best to opt for a recipe that is already developed to be that way.

Ingredient swaps
PUMPKIN. You need pure pumpkin puree for this recipe and it cannot be subbed with pumpkin pie filling. Pumpkin pie filling already contains all the spices, sugar and other ingredients in pumpkin pie, so be sure you’re using just plain pumpkin puree for these muffins. You will need just shy of one 15 ounce can.
FLOUR. This recipe calls for gluten free all purpose baking flour, which you cannot sub for almond, coconut, oat or another type of flour. You can use regular all purpose flour (non gluten free), but please do not try using another gluten free flour such as almond, oat etc. I like the Bob’s Red Mill 1:1 Baking Flour, just make sure whatever you use has xanthan gum!
SUGAR. You can sub the light brown sugar for coconut sugar, but I don’t recommend subbing the white sugar for coconut sugar. The muffins will be a very dark color and they may not rise as well. You can always try my healthy sweet potato muffins if you want a lower sugar option!

How to store and freeze
Once prepared, these gluten free muffins will keep for about 3 days at room temperature, or 5 days in the fridge. They can get a bit soggy if put in an air tight container because of the pumpkin, so I suggest leaving them in a container with the lid slightly ajar or covered loosely with foil.
You can freeze these gluten free pumpkin muffins after they bake. Be sure to let them cool completely, then transfer to a freezer safe bag and freeze for up to one month. Let them defrost in the fridge overnight, then warm up in the oven or microwave.

Try these snack recipes next!
- Matcha Muffins
- Almond Flour Blueberry Muffins
- Gluten Free Zucchini Muffins
- Gluten Free Pumpkin Bread
- Protein Muffins
- Mini Chocolate Chip Muffins
Lastly, if you want more recipes straight to your inbox, be sure to subscribe to my email list. As always, tag me on instagram if you make this recipe so I can see your creation!

Gluten Free Pumpkin Muffins
by: claire cary
Ingredients
Wet
- 2 large eggs
- 6 tablespoons melted butter or coconut oil
- 1 ½ cups pure pumpkin puree
- ⅔ cup white sugar
- ½ cup light brown sugar
- 2 teaspoons vanilla
- 1 teaspoon apple cider vinegar
Dry
- 1 ¾ cup gluten free all purpose baking flour
- 1 ½ teaspoons baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- ½ teaspoon cinnamon
- 2 ¾ teaspoons pumpkin pie spice
- ½ cup chocolate chips
Streusel
- 4 tablespoons brown sugar
- 4 tablespoons gluten free all purpose flour
- 2 tablespoons butter or coconut oil softened
- ¼ teaspoon pumpkin pie spice
Instructions
- Preheat the oven to 350 degrees Fahrenheit. Line a muffin tin with 12 liners and set aside.
- In a large mixing bowl, whisk together all wet ingredients until smooth.
- Whisk in the dry ingredients, making sure to spoon and level the flour.
- Fold in the chocolate chips.
- Scoop the batter into a muffin tray, filling each to the top to ensure nice round muffin tops.
- In a small dish, combine the sugar, flour and pumpkin pie spice. Cut in the butter or coconut oil with a fork until crumbly.
- Use your fingers to sprinkle the streusel on top of the muffins. Bake for 28-32 minutes or until a toothpick comes out clean.
- Let cool for about 15 minutes in the tray, then remove and transfer to a wire rack to finish cooling.
Notes
Comments
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I made this into a cake with cacao and chocolate chips without the pumpkin spices! It was a hit!
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Wow these were so fantastic! I used coconut oil and subbed 1 egg for a flax egg because I like the texture flax adds and feel it holds moisture well. They were very moist and flavorful; it’s a perfect recipe!
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Love it! Thanks, Liza!
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These were sooooo good. I made them almost exactly as the recipe says, but subbed some almond flour for a small portion of the GF. Added dried cranberries instead of chips, and used a method of baking from another favorite recipe where you bake hot for the first five minutes then reduce for the rest, which gives the muffins a nice high dome. My daughter said they were PERFECT.
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Wow!! These are incredible! My family is not gluten free but they LOVE them! I used plant based butter to make them dairy free as well and sooooo delicious!! Thank you!
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Amazing, thank you Denise!
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Was craving a pumpkin treat and this recipe delivered. It was simple to make and satisfied my craving. I skipped the topping to cut down on the sugar. I did not miss it.
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Perfect, thanks Molly!
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Have not tried yet, recommendations for an egg substitute? Making for my niece with an egg allergy amongst other things.
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I’d try a store bought egg replacer like Bob’s Red Mill or an extra 6 tablespons of pumpkin.
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These turned out amazing! Even with my tweaks, which I was nervous would not work. I replaced all of the sugar with a stevia/erythritol baking blend to make them low-sugar. I also ran out of my 1:1 GF flour and had to replace the last 1/2 cup with almond flour. They still turned out great! I’m sure they’d be even better with the original ingredients, but I was thrilled with my result. Thanks for the great recipe!
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Easy recipe! Didn’t taste GF. I love gingerbread spicy so I doubled the spices here too and was not disappointed. I also used mini chocolate chips!
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Thank you, my favorite kind of review!
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can i use oat flour instead of gf all purpose flour?
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I don’t recommend that here! You can try my sweet potato muffins instead!
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These muffins were very good! I like that they’re not too sweet!
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Thank you, Laurie!
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Picky eaters approved 👌.
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The best kind of comment!
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We rate these a 5. My husband even loves them. Thanks so much for putting this and so many more of your recipes out there. Keep them coming.
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Thank you, Pam!
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These came out so good. I left out chocolate chips, but still so good. If I made this into a loaf, how long would I cook it in the oven?
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I haven’t tried it as a loaf, but my guess would be about 55-60 minutes.
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Needed a higher oven temperature.375F would have been more normal for muffins. After 32+4 minutes they still were not completely done. Tasted good.
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These are incredible! I made 2 batches last week and gave some to neighbors and family, my kids devoured them, everyone loved them. I’m making more right now! Perfect texture, can’t even tell they are GF.
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Thank you, Andrea!
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