These are the best gluten-free pumpkin chocolate chip muffins! They are so easy to make and these delicious muffins are also dairy-free, nut free, and paleo, but they are so good that you would never know it! They are the perfect fall breakfast or snack.

Fall means it's time for all things pumpkin including edible pumpkin cookie dough and gluten free chocolate chip cookie bars and the delicious pumpkin muffin recipe I am sharing with you today!
Table of Contents
Why you will love these muffins:
- The taste! These muffins have the best flavour and are nice and moist with hints of cinnamon. They do not have a strong pumpkin flavour, so even if you don't like pumpkin you will still love them.
- They are quick and easy to make and since they are made in one bowl the clean up is so simple.
- Besides being gluten-free these muffins are also healthy, dairy-free, nut free, grain free, refined sugar free, and paleo.
Want an even easier pumpkin treat? Make pumpkin mousse or pumpkin Rice Krispie treats instead.
Ingredients:
For the exact measurements refer to the recipe card later in this post.
Jump to the Recipe- Dry ingredients: tapioca flour, coconut flour, baking soda and salt. Note that tapioca flour and cassava flour are not the same thing, so don't confuse the two.
- Spices: ground cinnamon, nutmeg, cloves, allspice and sea salt - this combination of spices gives these muffins that perfect fall flavour.
- Wet ingredients: full fat coconut milk, coconut oil, vanilla extract, maple syrup and pumpkin puree. Don't use pumpkin pie filling as it's too sweet.
- Eggs: a key ingredient to help these muffins rise. I have not tried using any egg replacers for this recipe and do not recommend it.
- Chocolate chips: I like using dark chocolate chips but you can use any type of chocolate chips that you prefer. To keep the muffins refined sugar free use chocolate chips sweetened with coconut sugar.
Recipe variations and add ins:
- For more texture add some chopped nuts such as pecans or walnuts.
- You could add a chocolate drizzle like I did for the photos by melting a dark chocolate bar with 1 tablespoon of coconut oil and then drizzling it over the muffins once they are done baking.
How to make gluten-free pumpkin chocolate chip muffins:
- Step 1: Preheat your oven to 350 degrees Fahrenheit. While the oven is heating, add all the ingredients, except the chocolate chips, to the bowl of your standing mixer and blend well until the batter is smooth.
- Step 2: Stir in the chocolate chips by hand.
- Step 3: Line a muffin tray with parchment paper muffin cups and transfer the batter to the muffin cups, and fill each cup until level with the tray. Bake for 30-35 minutes, until a toothpick inserted inside comes out clean.
- Step 4: Let the muffins cool, then enjoy!
Top tips:
- If you don't have a standing mixer you can mix the ingredients by hand using a whisk or spoon.
- Don't try swapping the maple syrup for honey. I have tried it and the muffins don't taste as good.
- Use room temperature eggs for best results.
- Let the muffins cool completely before serving.
- Storage: store these muffins in an airtight container in the fridge for up to 7 days. These muffins freeze really well for up to 3 months in a freezer safe bag or container.
Gluten-free pumpkin chocolate chip muffins FAQs:
No! Cassava flour and tapioca flour are very different flours. Cassava flour requires way more liquid ingredients to bake properly so if you tried using it these muffins would turn out very very dry.
I do not recommend trying to swap the coconut flour for another flour. These muffins won't turn out.
I do not recommend it. Pumpkin pie filling is already sweetened and flavours with spices so it would change the taste of these muffins completely.
Despite being dairy free these pumpkin muffins are not vegan because they contain eggs. I do not recommend trying to omit the eggs from this recipe to make these muffins vegan. I don’t think they will turn out as coconut flour requires eggs to bake and rise properly.
Yes! Canned pumpkin (not pumpkin pie filling) is just cooked pumpkin that has been pureed.
Other gluten-free muffin recipes you will love:
Recipe
Gluten-Free Pumpkin Chocolate Chip Muffins
Ingredients
Muffin Ingredients
- 1 cup coconut flour
- 1/2 cup tapioca flour
- 1 tablespoon ground cinnamon
- 1 teaspoon ground nutmeg
- 1 teaspoon baking soda
- 1/4 teaspoon ground cloves
- 1/4 teaspoon ground allspice
- pinch sea salt
- 1 cup cooked pumpkin puree (canned or homemade)
- 3/4 cup full fat coconut milk
- 1/3 cup maple syrup
- 1/4 cup coconut oil, melted
- 1 tablespoon organic vanilla extract
- 4 large eggs (preferably organic and free range)
- 1 cup dark chocolate chips
Instructions
Muffin Instructions
- Preheat your oven to 350F.
- Line a muffin tray with parchment paper muffin liners.
- Add all the ingredients for the muffins, except for the chocolate chips, into the bowl of your standing mixer.
- Blend well on low until the ingredients are smooth.
- Stir the chocolate chips in by hand.
- Transfer the batter to the muffin cups, and fill each cup until level with the tray.
- Place the tray in the oven and bake for 30-35 minutes, until a toothpick inserted into a muffin comes out clean.
- Serve and enjoy!
Notes
- This recipe yields 12 muffins.
- Allow the muffins to cool before eating.
- You can use either canned or homemade pumpkin puree.
- Nutritional values are an estimate and will vary depending on the specific ingredients you use.
Mary
Can I use egg substitute?
Erin Carter
Hey Mary! I've never tried the recipe with an egg substitute. Typically cassava flour needs eggs in order to bake properly but if you do decide to give it a try please let us know how it goes.
Joanne
These muffins look delicious! I don't use tapioca flour; can almond flour be used instead?
Erin Carter
Hey Joanne!
So tapioca flour and almond flour are very different. I wouldn't recommend trying to sub almond for tapioca. I don't think it will work out.