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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These were yummy and so easy to make! I did 1c gf flour and 3/4 c oat flour to add in some whole grains and they were perfect. They don’t even taste gluten free which is always a win in our house!
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Love to hear that! Thanks, Heather!
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Great recipe and tasted delicious with my friends over a coffee.
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Sounds perfect!
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This recipe is so good! It’s easy to make, has great pumpkin flavor, and tastes delicious even without the chocolate chips. Even my picky siblings like them, so that’s a win!
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Great recipe. I realized halfway I only had one cup of butternut squash purée. So instead of sugar, I added half cup maple syrup and maybe 2 tablespoons of brown sugar using butternut squash made the batter more sweet and what I added was just perfect for sweetness
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Yum, so glad you made it work for you!
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Delicious!!
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LOVE! I have made this several times. It even works with 1/2 the sugar called for! I can’t ever seem to get the crumble right, but they’re just as good (and sooooo good!)
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These are insane. In the best way. I made these for a gal pal gathering and they ate them like starving wild animals. Make these!
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Haha amazing, thanks Chelsea!
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These muffins turned out great! Being allergic I needed a dairy free, GF, eggless option, so I used the coconut oil per the recipe, used reduced allergen choco chips and substituted the eggs for “JUST EGG” plus 1Tablespoon Cornstarch (for consistency). They are hands down the best reduced allergen muffins I’ve had. Thanks a bunch! Saved me a TON of frustration experimenting with frankenmuffins.
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Love it! Thanks, Nena!
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These are the best gluten free pumpkin muffins!! You wouldn’t even know they are gluten free. I have made them multiple times in the past two months. I even made them without the chocolate chips because I ran out and they were still delicious. This is officially my fall go to!
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Perfect! Thank you, Andrea!
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These pumpkin muffins are delicious! I made them exactly by the recipe. I used King Arthur Measure for Measure GF flour and the texture was smooth and moist. I liked the slightly crispy streusel on top. Thank you Claire!
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Thank you, Sarah! So happy you enjoyed it.
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I made this recipe exactly as written with the exception of the crumble topping (time constraints). They turned out perfectly moist and sooo delicious! My family also gave this one a 5 star rating. Thank you for sharing this wonderful treat!
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Love it! Thank you, Kimberly!
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Made them without the topping! So so delicious! I brought them to a gathering and they were loved by the gluten free a regular diet individuals alike!
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Love it! Thanks, Brit!
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