Gluten Free Pumpkin Muffins with Chocolate Chips

Last updated September 5, 2024 By Kelly Nardo | 2 Comments
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Healthy gluten-free pumpkin muffins are light, fluffy, and packed with pumpkin spice and chocolate chips! They are ready in 35 minutes and make a healthy muffin recipe for breakfast, a snack, dessert, or meal prep.
Prep: 13 minutes
Cook: 22 minutes
Total Time: 35 minutes
Servings 10 muffins
4.67 from 3 votes

It’s officially September and that means all things pumpkin! We are starting off the season with a bang with these gluten-free pumpkin muffins with chocolate chips!

They are based off of my pumpkin bars, but I tweaked the recipe a tad to make the most moist, tender, and fluffy muffins. Plus, they are made with simple ingredients, lightly sweetened, and full of pumpkin flavor that compliments the chocolate so well.

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Overhead shot of six pumpkin chocolate chip muffins in a muffin tin.

I like using a 1:1 gluten-free flour blend with xanthan gum, as I find it works the best and gives you a texture very similar to traditional all-purpose flour. You can find it in most stores and it makes an easy 1-to-1 substitute for gluten-free baking.

These pumpkin chocolate chip muffins can be enjoyed as a snack, with breakfast, or as a dessert. Plus, for your leftovers, pop them in the microwave for 10-25 seconds to warm through and let the chocolate melt. 

Why we love this gluten-free pumpkin muffin recipe

  • they come out light, fluffy, and perfectly moist!
  • made from 11 simple ingredients and so delicious!
  • lightly sweetened – we are using just 2 tablespoons of maple syrup plus some chocolate chips.
  • gluten-free – but I promise no one would even know!
An overhead shot of chocolate chip pumpkin muffins in a muffin tin. One of the muffins is turned on its side with a bite taken out of it.

Are pumpkin muffins healthy?

Traditional muffins are usually prepared with a decent amount of simple carbs and sugar. By eating them by themselves, they can spike your blood sugar, causing it to crash and leaving you tired, hungry, and moody. Although pumpkin is a low calorie food full of vitamin A, vitamin K, potassium, manganese, and fiber, it is in muffin form.

Of course, all foods can be enjoyed in moderation. Furthermore by making them at home, you can easily customize them to fit your liking and nutrition goals.

These gluten-free muffins are lightly sweetened with only 7 grams of sugar per muffin. Also, they have some fat and a little protein to help slow down digestion and help prevent blood sugar spikes and crashes.

Gluten free pumpkin muffins ingredients

  • gluten-free baking flour – make sure to use a 1:1 gluten-free baking flour. I love Bob’s Red Mill.
  • pumpkin pie spice
  • baking soda
  • baking powder
  • salt
  • pumpkin puree – make sure to use 100% pumpkin and not pumpkin pie filling.
  • eggs
  • butter
  • maple syrup
  • vanilla bean paste – a pumped-up version of vanilla extract. Both work the same though.
  • mini chocolate chips – mini for maximum chocolate flavor!
White marble counter with a bowl of pumpkin puree, a bowl of vanilla bean paste, 2 brown eggs, a bowl of maple syrup, a bowl of mini chocolate chips, a bowl of baking soda and powder, a bowl of salt, a bowl of cubed butter, a bowl of spices, and a bowl of flour.

How to make pumpkin muffins

  1. Preheat the oven to 350 degrees Fahrenheit. Line a muffin tin with 10 nonstick paper muffin liners or reusable silicone liners.
  2. Mix your dry ingredients. Add your flour, pumpkin pie spice, baking soda, baking powder, and salt in a medium bowl and whisk to combine.
  3. Mix your wet ingredients. In a separate medium-large mixing bowl, add your pumpkin puree, eggs, butter, maple syrup, and vanilla bean paste and mix well to combine. Next, add your dry mixture to your wet mixture and stir to combine. The batter should be pretty thick. Finally, fold in the chocolate chips. I like to save 1-2 tablespoons worth to sprinkle on top of the muffins.
  4. Bake. Using a cookie scoop, or about 2 1/2 tablespoons worth, distribute the muffin batter between the 10 liners. Sprinkle the muffins with remaining chocolate chips. Bake for 22-25 minutes until golden brown on the top. You can check doneness by inserting a toothpick in the center. It should come out clean with a few moist crumbs. Let cool for a couple of minutes.
  5. Enjoy!
Muffin tin with muffin liners filled with uncooked muffin batter with chocolate chips in it.

Storage

  • refrigerator – first, let them cool completely. Add to an airtight container or silicone bag and store them in the fridge for up to a week.
  • freezer – let cool completely and place on a large plate or baking sheet. Place in the freezer and let freeze for 2 hours until hardened. This will help ensure they freeze individually and won’t stick together. Once frozen, transfer to a large freezer bag (we love reusable silicone ones) and freeze for up to 3 months. Let them thaw at room temperature or overnight in the fridge. They can be warmed up in the microwave if desired.
Overhead shot of healthy pumpkin muffins with chocolate chips in a muffin tin.

Substitutions and additions

  • gluten-free baking flour – all-purpose flour will work the same. You could try whole wheat flour or oat flour, but I am not sure if the texture will come out the same. Coconut flour and almond flour will not work as their consistency is very different.
  • pumpkin pie spice – if you don’t have pumpkin pie spice, a mix of cinnamon, ginger, nutmeg, cloves, and allspice will work instead. You will need 1 1/2 tablespoons total.
  • pumpkin puree – make sure to use 100% pumpkin and not pumpkin pie puree.
  • eggs – I haven’t tried an egg substitute so I’m not sure if they will work. The eggs help keep them moist and have a light texture.
  • butter – ghee should work the same. If you want a dairy-free option, you can try coconut oil, but I haven’t tried it.
  • maple syrup – any kind of liquid sweetener will work the same (honey, agave…).
  • vanilla bean paste – vanilla extract will work the same.
  • mini chocolate chips – I like using mini for more chocolate, but regular-size ones will work. Milk or dark chocolate chips work as well. Use dairy-free chocolate chips if needed.

In addition, here are some ingredients to add to change up the flavor:

  • chopped nuts – walnuts or pecans would be great. Stir them into the batter.
  • dried fruit – raisins or cranberries would work well.
  • cacao powder – to make them extra chocolatey, stir some cacao powder into the batter.

More healthy muffin recipes

If you love quick and easy meals and want to learn how to build a balanced plate, check out our FREE How to Build a Balanced Plate Guide!

Close up of a gluten free pumpkin muffin with chocolate chips with a bite taken out of it. It is sitting on the muffin wrapper. Behind it is a muffin tin filled with more muffins.
Close up of a gluten free pumpkin muffin with chocolate chips with a bite taken out of it. It is sitting on the muffin wrapper. Behind it is a muffin tin filled with more muffins.
4.67 from 3 votes

Gluten Free Pumpkin Muffins

Author: Kelly Nardo
Healthy gluten-free pumpkin muffins are light, fluffy, and packed with pumpkin spice and chocolate chips! They are ready in 35 minutes and make a healthy muffin recipe for breakfast, a snack, dessert, or meal prep.
Print Recipe Pin Recipe
Course: Breakfast, Snack
Calories: 169kcal
Protein: 3g
Carbs: 21.9g
Fat: 8.1g
Prep Time: 13 minutes
Cook Time: 22 minutes
Total Time: 35 minutes
Servings: 10 muffins

equipment

ingredients

instructions

  • Preheat the oven to 350 degrees Fahrenheit. Line a muffin pan with 10 nonstick paper muffin liners or reusable silicone liners.
  • Mix your dry ingredients. Add your flour, pumpkin pie spice, baking soda, baking powder, and salt in a medium bowl and whisk to combine.
  • Mix your wet ingredients. In a separate medium-large mixing bowl, add your pumpkin puree, eggs, butter, maple syrup, and vanilla bean paste and mix well to combine. Add your dry mixture to your wet mixture and stir to combine. The batter should be pretty thick. Fold in the chocolate chips. I like to save 1-2 tablespoons worth to sprinkle on top of the muffins.
  • Bake. Using a cookie scoop, or about 2 1/2 tablespoons worth, distribute the batter between the 10 liners. Sprinkle the muffins with remaining chocolate chips. Bake for 22-25 minutes until golden brown on the top. You can check doneness by inserting a toothpick in the center. It should come out clean with a few moist crumbs. Let cool for a couple of minutes.
  • Enjoy!

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nutrition

Nutrition Facts
Gluten Free Pumpkin Muffins
Amount Per Serving (1 muffin)
Calories 169 Calories from Fat 73
% Daily Value*
Fat 8.1g12%
Saturated Fat 4.7g29%
Polyunsaturated Fat 0.4g
Monounsaturated Fat 1.6g
Cholesterol 50mg17%
Sodium 273mg12%
Potassium 110mg3%
Carbohydrates 21.9g7%
Fiber 1.8g8%
Sugar 6.8g8%
Protein 3g6%
Vitamin A 269IU5%
Vitamin C 1mg1%
Calcium 61mg6%
Iron 1.3mg7%
* Percent Daily Values are based on a 2000 calorie diet.
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4.67 from 3 votes (3 ratings without comment)

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2 Comments

    1. Hey, Ellie! It will depend on how hot your house is. If it’s pretty cool, I would say 2 days or so. If it’s warm, I would suggest storing them in the fridge for the best results.