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These gluten free pumpkin muffins are filled with  pumpkin pure, fall spices and chocolate chips. Enjoy a delicious muffin in the morning this fall without  gluten!

Love gluten-free muffins? You have to try healthy banana muffins or gluten-free morning glory muffins. Use gluten-free flour in these mini chocolate chip muffins too!

gluten free pumpkin muffins with chocolate chips on top
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After making grain free pumpkin granola recently, I figured now is better than ever to keep the pumpkin train rolling. We’re in mid-September and for me that’s full force pumpkin everything.

I love pumpkin not only because it’s a fall baking staple, but also because it’s super healthy and works so well in so many healthy baking recipes. It’s a perfect swap for eggs or butter in recipes and adds tons of flavor to any baked good.

I made these gluten-free pumpkin muffins over the weekend and packed them up for a family vacation in the Outer Banks this week. It was soooo hard not to eat them all in the car on the way down.

gluten free pumpkin muffins in a muffin tin

My family loves when I bring all my baked goods to family gatherings. Because what’s better than sharing food with family?! I typically freeze a lot of my recipes so I have them on hand when I go to a family event or a party with friends. That’s a pro tip people!

Or in this case muffin/dessert. These gluten free pumpkin muffins are interchangeable between breakfast and dessert in my opinion. It’s something sweet to enjoy after dinner or an excuse to each chocolate for breakfast.

a pumpkin muffin with a bite taken out

What I love about these Gluten Free Pumpkin Muffins

  • Taste: These muffins are packed with pumpkin spice flavor! The richness from the melted butter and brown sugar adds a killer combo to the tenderness from the eggs, pumpkin and spices. Oh, and those melty chocolate chips are insanely good.
  • Texture: They’re light, fluffy, tender and soooo soft when you take a bite. I love to warm mine back up in the microwave after cooling to make them extra soft and melty.
  • Ease: These are SO easy. I wen there with the all caps because they only require one bowl. Anything that means I only need to clean one dish deserves extra love.
  • Appearance: Just look at those chocolate chip-studded tops! They’re so perfect. Not to mention the pumpkin and orange color just screams fall.
gluten free pumpkin muffin recipe

I have to admit, muffins are some of my favorite recipes to bake. Mostly because a lot of them only require one bowl or the blender, but also because I love the puffy tops and soft centers.

They’re one of the most versatile staples (along with cookies). If you have a really good base to a muffin recipe you can pretty much add in any flavor combo or mixtures/additions to anyone’s liking.

The Best Muffin Baking Tip

Baking muffins at a really high temperature right away allows them to puff up really tall right off the bat and the lower temperature then bakes them all the way through. This is how you get that signature bakery muffin look. If you’re feeling extra fancy you can even add sparkling sugar to the tops✨.

a gluten free chocolate chip pumpkin muffin with a bite taken out laying on its side

How to Make Gluten Free Pumpkin Muffins

Make the muffin batter

  1. Using a whisk, mix the wet ingredients until combined. Add the dry ingredients and gently fold/whisk until the majority of the lumps are gone, being careful not to overmix.
  2. Fold in the chocolate chips until they’re evenly distributed through the muffin batter. I like to reserve a few to place on the top of each muffin before baking so they look even prettier after they’re baked.

Fill muffin tins and bake

  1. Place the muffin liners in the muffin tin and spray them all with non stick spray so they don’t stick to the muffins once they’re baked. You’re going to fill the muffin tins all the way full with the batter for this recipe. Fill them all the way to the brim so they’re almost overflowing with batter then add a few extra chocolate chips on top.
  2. Bake the muffins at 425°F for 5 minutes. After 5 minutes, reduce the oven temperature to 350°F, leaving the muffins in the oven, and bake them the rest of the way through, about 15-18 more minutes. Allow the muffins to cool slightly then transfer to a wire rack to cool completely.

Dieatary Modifications

Dairy-free: use a plant based vegan butter instead of regular butter. Coconut oil would work too, but the butter has much more flavor.

Egg free: make flax eggs or use Bob’s Red Mill egg substitute.

Vegan pumpkin muffins: follow the instructions above for both dairy-free and egg-free.

3 gluten free pumpkin chocolate chip muffins stacked on top of each other

If you love this recipe, don’t forget to leave a star review below and tag us on Instagram. And if you’re looking for a gluten-free pumpkin muffin recipe made with almond flour, check out our healthy pumpkin muffins.

More pumpkin recipes

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4.35 from 138 votes

Gluten-Free Pumpkin Muffins

Prep: 10 minutes
Cook: 25 minutes
Total: 35 minutes
These gluten free pumpkin muffins are filled with  pumpkin pure, fall spices and chocolate chips. Enjoy a delicious muffin in the morning this fall without  gluten!

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Servings: 12 muffins


  • 2 large eggs
  • 3/4 cup lightly packed brown sugar or coconut sugar
  • 1/4 cup granulated sugar
  • 1 cup pumpkin puree
  • 3/4 cup unsalted butter melted and slightly cooled
  • 1 teaspoon vanilla extract
  • 1 3/4 cups 1:1 gluten free flour I use Bob’s Red Mill
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 2 teaspoons pumpkin pie spice
  • 1 cup semi-sweet chocolate chips


  • Preheat oven to 425°F. Line a 12 count muffin pan with liners and spray them nonstick cooking spray and set aside.
  • In a large bowl, whisk the eggs, brown sugar, granulated sugar, pumpkin puree, melted butter and vanilla until combined. Add the gluten-free flour, baking powder, baking soda, salt and pumpkin pie spice to the wet ingredients and gently whisk until just combined, being careful not to over mix. Add the chocolate chips, reserving a few for the tops of the muffins, and fold in gently. The batter will be thick.
  • Fill the muffin cups all the way full and almost overflowing. Add the reserved chocolate chips to the top of the unbaked muffins.
  • Bake the muffins 5 minutes at 425°F then, keeping the muffins in the oven, reduce the oven temperature to 350°F. Bake for an additional 15-18 minutes or until a toothpick inserted in the center comes out clean.
  • Remove the muffins from the oven and allow to cool in the pan for 5-10 minutes then transfer to a wire cooling rack to cool completely.
  • Store muffins in an air tight container at room temperature for up to 5 days or in the freezer for up to 3 months.
Last step! If you make this, please leave a review letting us know how it was!


Storage: allow the gf pumpkin muffins to cool completely then store in an airtight container in the fridge for up to one week. To freeze, wrap the muffins in plastic wrap and place in a freezer bag and store in the freezer for up to 4 months. Thaw overnight in the fridge and enjoy cold or warm in the microwave.
Gluten-free flour blend: our favorite is bob’s red mill, but you can use any 1:1 gluten-free flour that includes xanthan gum.



Serving: 1muffin | Calories: 378kcal | Carbohydrates: 34.9g | Protein: 5.1g | Fat: 20.6g | Cholesterol: 61.5mg | Sodium: 221mg | Fiber: 2.6g | Sugar: 29.5g

Nutrition information is automatically calculated, so should only be used as an approximation.


  1. Janice Minchin says:

    Can these be done WITHOUT EGGS, I have an egg allergy. I often use banana as a substitute. They look,and sound wonderful.

    1. Molly Leonard says:

      Hi Janice! Yes, you can definitely sub out eggs here. Use 1/4 cup of mashed banana to sub out one egg. Or you could to 1 tablespoon of ground flax seed with 3 tablespoons of water to sub out one egg! So for this recipe it would be 1/2 cup mashed banana or 2 tablespoons ground flax seed!

  2. Bethany says:

    Pumpkin chocolate chip muffins are the best! Yum!

  3. Jocelyn (Grandbaby Cakes) says:

    These muffins looks awesome!!

    1. Molly Leonard says:

      Thanks Jocelyn!