Gluten-Free Pumpkin Chocolate Chip Muffins

Gluten-Free Pumpkin Chocolate Chip Muffins are so tender, soft, and delicious! With cinnamon spice and bursts of chocolate chips in every bite, you will absolutely love them this and every season! We make them every fall and they are a hit every time!

Hey there pumpkin! We all love it – September 1st rolls around and for the next 3 months we are making all the pumpkin muffins, breads, fall drinks, and cookies we can get our hands on!

These healthy gluten-free pumpkin chocolate chip muffins are on the top of the baking list. Made in one-bowl, with a soft fluffy texture and healthier ingredients than any store-bought version.

Jump to:
  • Why this is the best recipe
  • Key Ingredients
  • Recipe Directions
  • Storing Pumpkin Muffins
  • Substitutions
  • Tips
  • Frequently Asked Questions
  • More Healthy Pumpkin Recipes You May Enjoy!
  • Gluten-Free Pumpkin Chocolate Chip Muffins

Why this is the best recipe

  • These gluten-free pumpkin chocolate chip muffins are healthy! We use gluten-free flour, dairy-free ingredients, and coconut sugar in place of processed sugar. And we’ve got a few ingredients and tips that keep gluten-free pumpkin muffins from getting dry. These stay soft!
  • It’s a versatile recipe! Try swapping out chocolate chips for white chocolate chips or a mixture of dried cranberries too. Or leave the muffins without the chocolate like these gluten-free pumpkin muffins.
  • Can be turned into a quick bread! Instead of baking in a muffin pan, these chocolate chip pumpkin muffins can easily be turned into a bread loaf.

Key Ingredients

  • pumpkin puree – not pumpkin pie mix. You want 100% pumpkin that does not have added sugars and spices.
  • 3 large eggs – aim for free range and organic as much as possible for a healthier egg. The eggs help keep these muffins extra fluffy!
  • avocado oil – or olive oil.
  • coconut sugar – or a low glycemic sugar such as Xylitol or Monk fruit sugar.
  • vanilla – adds beautiful vanilla flavor that compliments pumpkin.
  • gluten free flour – we test this recipe using Bob’s Red Mill 1-1 gluten-free all purpose flour and with my homemade gluten-free flour recipe from my gluten-free baking cookbook. Both flours used have turned out perfect!
  • baking powder
  • baking soda
  • cinnamon
  • pink Himalayan salt – we use pink Himalayan salt for health benefits but you can also use regular table salt.
  • chocolate chips – choose your favorite and try semi-sweet, milk chocolate, or dairy-free chocolate morsels.

Recipe Directions

As always, be sure to check out the full recipe details in the recipe card below.

Step 1: In a large bowl combine the dry ingredients then add in the wet ingredients. Use a whisk to mix everything together.

Step 2: Fold in the chocolate chips. Then add the batter to a muffin pan.

Step 3: Add muffin or cupcake liners in a muffin pan and spray with cooking oil, then fill each equally with the pumpkin muffin batter.

Step 4: Bake the muffins in a preheated oven at 350 degrees F for 24-28 minutes or until they are set at the top and a toothpick inserted comes out clean.

Storing Pumpkin Muffins

You can store and free gluten-free pumpkin chocolate chip muffins if you are not going to eat them all at once. They store well on the counter in a closed container for 2-3 days. After that they start to get hard and loose flavor, so they are best enjoyed right away.

To freeze gluten-free chocolate chip pumpkin muffins, place them in a sealed freezer zip bag. Remove as much air as possible and store them in the freezer for about 1 month. To freeze for longer wrap each muffin individually with plastic, then place them in a freezer bag. Seal closed, removing as much air as possible. They will last this way up to 3 months.


This pumpkin recipe uses healthy sugar and gluten-free flour. You can try these substitutions as well:

  • Swap gluten-free flour for spelt flour or oat flour if wheat and gluten is not an issue. Spelt flour is has a lower amount of gluten (almost no gluten) than wheat flours but spelt does contain wheat so it is not great for celiac. I have not tried this recipe using almond flour.
  • Substitute avocado oil for another oil such as olive oil or melted coconut oil.
  • Coconut sugar can be replaced with light brown sugar (don’t pack it), or regular sugar.


  • Spray cupcake liners with cooking oil first. This helps the gluten-free pumpkin chocolate chip muffins not to stick to the liners. Alternatively you can use a silicone muffin pan and skip using the liners, but make sure to spray the pan first.
  • Mix, mix, mix! Mix the batter enough so that there are no visible chunks of flour or leavening agents.
  • Don’t overbake these gluten-free pumpkin chocolate chip muffins. Overbaking will cause the muffins to dry out and they will not be as moist. They most-likely only need to bake for 24 minutes (mine come out perfect in my oven at this time).

Frequently Asked Questions

Can I use pumpkin pie mix for pumpkin muffins?

No, do not use canned pumpkin pie mix for pumpkin muffins and any of my baked pumpkin recipes. Pumpkin puree is pure pumpkin without the sugar and spices. When making pumpkin muffins from scratch we add the sugar and spices within the recipe steps.

Are gluten-free pumpkin chocolate chip muffins healthy?

Yes! These gluten-free chocolate chip pumpkin muffins are made with healthy ingredients including low glycemic sugar, gluten-free flour, eggs for protein, and avocado oil which is a great source of healthy monosaturated fat.

More Healthy Pumpkin Recipes You May Enjoy!

I hope you enjoy this gluten-free pumpkin chocolate chip muffin recipe! Follow along with me on INSTAGRAM, PINTEREST, FACEBOOK, YOUTUBE and TWITTER for a feature and for more recipe inspiration! And don’t forget to give the recipe a star rating in the recipe area and leave a comment below.

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