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Gluten Free Chocolate Chip Pumpkin Muffins (Vegan)

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Bake up some moist gluten free and dairy free chocolate chip pumpkin muffins for cozy fall weekends! Our muffins have a delicious streusel topping and are also egg free and peanut free.

photo collage showing baked and unbaked gluten free pumpkin streusel muffins.

If you are craving moist and incredibly delicious pumpkin streusel muffins that are multiple allergy friendly, you’ve come to the right place. Our pumpkin muffin recipe is gluten free, dairy free, egg free, and peanut free, but they’re so delicious and will even stay moist the next day.

One of the problems we have ran into with our sorghum flour-based baked goods is that sometimes they could be rather dry the next day. I experimented with a blend of gluten free flours for these muffins and I discovered that using a blend helps these muffins stay moist the next day.

Our muffins are a bit different than some other muffin recipes because they don’t peak at the top of the muffin since we don’t use eggs in this recipe. This is normal for these muffins and doesn’t affect the taste of the recipe!

Our pumpkin muffin recipe is:

  • Gluten free
  • Dairy free
  • Egg free and vegan
  • Peanut free
  • Tree nut free and soy free (depending on which dairy free butter you use)
chocolate chip pumpkin streusel muffins split in half sitting on a white plate.

How to make our gluten free pumpkin muffins

Our vegan pumpkin muffins have a few steps, but they aren’t complicated to make. Here are the steps (this is just an overview, the full recipe card is at the end of the post):

  1. Preheat the oven to 350 degrees F and line a regular sized muffin tin with paper liners.
  2. In a small bowl, combine the streusel ingredients (brown sugar, gluten free flour, cinnamon, salt, and melted dairy free butter) and mix until crumbly. Set aside.
  3. In another small bowl, whisk together the dry ingredients (flours, spices, salt, baking powder, baking soda, and flaxseed). Set aside.
  4. In a large bowl, whisk together the wet ingredients (the pumpkin, brown sugar, oil, oat milk, and vanilla). Whisk until smooth, then stir in the mini chocolate chips.
  5. Add the dry ingredients to the wet ingredients and whisk until a smooth batter forms.
  6. Scoop the batter into the prepared muffin pan with liners, distributing the batter evenly.
  7. Stir the streusel topping mix again and sprinkle over the muffin batter, dividing it evenly between all the muffins.
  8. Bake in the oven for 20 minutes, a toothpick inserted in the muffin should come out clean (aside from any melted chocolate).
  9. Allow the muffins to cool in the pan for about 10 minutes then remove them to a cooling rack. These hold together the best when they have cooled for at least 15 minutes.
  10. Store leftover muffins in an airtight container or bag for up to 3 days.
overhead photo of pumpkin muffin batter in a glass bowl.

If you want a pumpkin muffin recipe that’s made without refined sugar or flour, check out our paleo pumpkin muffin recipe!

Recipe notes

Please note that our muffins don’t peak and sink slightly in the middle because we don’t have eggs in this recipe.

When you go to take these out of the oven, they are still done baking at 20 minutes even though they are slightly sunk and that’s normal for these muffins! The top may look slightly soft/wet as well, and that is normal, too. They will firm up more once they cool, but your toothpick inserted into the muffin should still come out clean aside from any melted chocolate.

If chocolate isn’t your thing, this recipe still tastes great without the mini chocolate chips, too. I made this recipe with chocolate chips and without them, and these muffins are delicious either way!

Make sure to use a gluten free baking flour or baking mix that has xanthan gum or some other binder in it (we used the King Arthur gluten free baking mix that has xanthan gum). Since these muffins don’t have eggs, they need additional binders, so between the flaxseed and the xanthan gum in the gluten free baking mix these hold together well once they are cooled.

overhead photo of a muffin pan with pumpkin muffin batter in white paper liners.

Also note that the King Arthur gluten free all purpose flour is slightly different than the King Arthur gluten free all purpose baking mix. The baking mix, which is what we used in this recipe, already has some baking soda and salt already in the mix.

If you’re using an all purpose gluten free flour that doesn’t have baking soda or salt in it you should still be ok since this recipe has enough of both to make up for any that the flour/baking mix may not have.

The salt is important as a natural flavor enhancer even in sweet recipes, so I don’t recommend leaving that out regardless of the flour or baking mix you’re using.

Can I skip the flaxseed in this recipe?

Because our muffins have some xanthan gum in them from the gluten free flour, this helps the muffins hold together a bit.

But I found that the batches of muffins I made without the flaxseed still ended up more crumbly and didn’t hold together as well as the batches I made with the ground flaxseed, so I recommend using the ground flaxseed as an additional binder since we didn’t use eggs.

If you don’t have ground flaxseed on hand, you can definitely make these muffins without it, just be aware that the muffins will be slightly crumblier than when you use the ground flaxseed.

hand holding a pumpkin muffin that is split in half.
Our pumpkin muffins without the chocolate chips

I love using the golden flaxseed then finely grinding it myself at home using my Nutribullet blender (I use my Nutribullet quite often vs a full sized blender). Using golden flaxseed vs regular dark flaxseed keeps baked goods looking their natural color rather than turning dark from the darker flaxseed meal.

It’s a personal preference and not absolutely necessary, but if you want to keep your baked goods lighter in color and looking closer to regular baked goods, I recommend using golden flaxseed.

Grinding your own flaxseed meal is also great for making your flaxseed last longer. I grind only as much as I need and keep both the whole flaxseed and ground flaxseed in the fridge. This also ensures that my ground flaxseed is finely ground to my preference.

Can I freeze these pumpkin chocolate chip muffins?

We did a freeze and thaw test with our muffins and they freeze and thaw very well. Once they are fully cooled, you can add the muffins to a freezer proof container or bag and put them in the freezer for up to three months.

When you go to thaw these, you can thaw them all at once on the counter at room temperature, or thaw them individually on the counter or in the microwave. If you thaw these in the microwave, it’s about 20-30 seconds at regular/full power for one muffin.

overhead photo of muffin batter in a metal muffin pan.
Pumpkin muffin batter with and without chocolate chips

Check out our other allergy friendly pumpkin recipes!

Gluten Free Chocolate Chip Pumpkin Muffins (Dairy Free)

Bake up some moist gluten free and dairy free chocolate chip pumpkin muffins for cozy fall weekends! Our muffins have a delicious streusel topping and are also egg free and peanut free.
Gluten free, vegan; Free of: eggs, peanuts, wheat, soy and tree nuts (depending on the type of dairy free butter you choose)
5 from 1 vote
Print Pin Rate
Course: Breakfast & Brunch
Cuisine: American
Keyword: chocolate chip pumpkin streusel muffins, gluten free pumpkin muffins, vegan pumpkin muffins
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 12 muffins
Calories: 225kcal





  • Preheat the oven to 350 degrees F. Line a muffin tin with muffin papers and set aside.

Streusel topping

  • Make the streusel: in a small bowl, stir together the brown sugar, gluten free flour, and cinnamon. Add the melted dairy free butter and stir again until mixed well and crumbly. Set aside while you make the muffins.


  • In a small bowl, whisk together the dry ingredients: the flours, ground flaxseed, baking powder, spices, salt, and baking soda. Set aside.
  • In a medium-large bowl, whisk together the wet ingredients: the brown sugar, dairy free milk, pumpkin, oil, and vanilla. Whisk until smooth.
  • Add the dry ingredients into the wet ingredients and whisk or stir together until a thick batter forms and everything is mixed well.
  • Add the mini chocolate chips and stir to combine.
  • Scoop the batter into the prepared muffin pan, evenly distributing all the batter between the muffins. Your muffin cups will be about half to 2/3 full.
  • Stir the streusel topping mix again and sprinkle over the muffin batter evenly between all the muffin cups.
  • Bake for 20 minutes. A toothpick inserted in the center should come out clean of batter (you may see melted chocolate on it and that's fine).
  • These muffins will sink slightly and may look a little damp on top under the streusel, but they are still done cooking at 20 minutes. These will firm up as they cool.
  • Remove the muffins from the oven and allow the muffins to cool in the pan for about 10 minutes, then remove from the pan to a cooling rack to cool completely. You can serve these slightly warm, but they hold together the best when they are completely cooled.
  • Store any leftover muffins in an airtight bag or container for up to 3 days. These also freeze and thaw well. Baked goods can be frozen for up to 3 months.


These muffins can be made without the chocolate chips if you want regular pumpkin muffins.


Calories: 225kcal | Carbohydrates: 33g | Protein: 2g | Fat: 10g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 5g | Trans Fat: 0.01g | Cholesterol: 0.4mg | Sodium: 253mg | Potassium: 154mg | Fiber: 3g | Sugar: 21g | Vitamin A: 1608IU | Vitamin C: 0.5mg | Calcium: 62mg | Iron: 1mg
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2 thoughts on “Gluten Free Chocolate Chip Pumpkin Muffins (Vegan)”

  1. Your pumpkin muffins sound delicious and those photos are amazing. I always love the flavor of pumpkin. I will definitely be giving these a try! Thanks.


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