Why This Recipe WORKS

  • Moist, never chalky. I specifically formulated this batter with enough moisture to balance the protein powder and keep the muffins tender.
  • The perfect sweetness. The coconut sugar, maple syrup, and chocolate chips give these muffins a balanced sweetness that doesn’t overpower the pumpkin spice.
  • A hearty muffin. The protein powder, eggs, and Greek yogurt give these muffins more staying power than a typical pumpkin muffin, making them a satisfying option for breakfast or a snack.
  • Easy to grab and go. These are one of my favorite muffins to make ahead. Once they’re completely cool, I store them in an airtight container or freeze them individually so they’re easy to grab whenever we need a quick, protein-packed snack.
A close-up of a pumpkin protein muffin with chocolate chips in a paper liner, surrounded by more muffins and a blurred background of milk and a decorative pumpkin.
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As much as I love breakfast recipes that are more sweet treats than healthy meals, I also enjoy creating healthier, protein-packed options that I can make on regular rotation in my house. We’ve made my pumpkin protein pancakes on repeat, so I knew I had to make a muffin recipe for pumpkin season this year!

These gluten-free pumpkin protein muffins are filling enough to keep me going on busy mornings, and my kids love them too! They’ve easily earned a spot among my favorite gluten-free pumpkin recipes.

What You Need

Here are a few notes on some of the key ingredients to make these gluten-free pumpkin protein muffins. Jump to the recipe card below for the exact measurements.

A variety of labeled baking ingredients are arranged on a counter, including eggs, chocolate chips, pumpkin puree, Greek yogurt, flours, spices, sweeteners, and baking powder and soda.
  • Vanilla protein powder. Protein powder gives these muffins an extra boost of protein while adding a little sweetness and vanilla flavor. Protein powders can vary quite a bit in how they bake, so I recommend using one you already know you like the flavor of. This is my favorite brand.
  • Pumpkin purée. I specifically created this recipe to use a whole can of pumpkin because there’s nothing worse than having ½ cup of pumpkin sitting in your fridge that you’re not sure what to do with. Be sure to use pure pumpkin purée, not pumpkin pie filling.
  • Greek yogurt. I use plain Greek yogurt to add even more protein while keeping the muffins moist. Its slight tang also balances the sweetness from the coconut sugar, maple syrup and chocolate chips.
  • Coconut sugar. I always have coconut sugar on hand because we use it as a filling for buckwheat crepes. If you don’t have coconut sugar you can use brown sugar no problem!

How to Make Gluten-Free Pumpkin Protein Muffins

Here’s an overview of how to make this recipe. You can jump to the recipe for the full instructions!

Hands holding a white mixing bowl with flour and brown sugar, using a whisk to combine the ingredients. Several empty bowls and dishes sit nearby on a light surface.

Whisk the dry ingredients. Combine the gluten-free flour, protein powder, coconut sugar, baking powder and soda, salt, and spices in a large bowl.

A mixing bowl with batter and a whisk, surrounded by eggshells, an empty can, small bowls, and a glass. The number 2 is in a gray circle in the top left corner.

Mix the wet ingredients. In a separate bowl whisk the pumpkin purée, yogurt, eggs, syrup, and vanilla until smooth.

Erin’s Tip

Protein powder naturally absorbs quite a bit of moisture, which is why this recipe uses a generous amount of pumpkin purée and Greek yogurt. I wouldn’t reduce either one—they help keep the muffins from turning out dry or chalky.

A person mixing flour into a yellow batter in a white bowl with a green spatula, step 3 in a recipe. Small bowls with ingredients and an open can are nearby on a light surface.

Combine mixtures. A rubber spatula makes it easy to blend the pumpkin mixture into the dry ingredients, leaving no streaks behind.

A hand pours chocolate chips from a white cup into pumpkin muffin batter in a mixing bowl with a green spatula. Several small bowls and an open can are nearby.

Add mix-ins. Once the batter is fully combined, fold the chocolate chips into the mixture.

Erin’s Tip

I like to use mini chocolate chips in many of my muffin recipes, like these gluten-free banana muffins, but I actually prefer regular-size semi-sweet chocolate chips in this recipe. I think they hold up better and create little pockets of chocolate in every bite!

Pumpkin protein muffin batter in a non-stick muffin pan, surrounded by various baking utensils and empty bowls on a light countertop.

Scoop and bake. Divide the batter evenly into the two muffin pans. Bake until a toothpick inserted into the center of a muffin comes out clean (about 25 minutes).

A muffin tray filled with twelve baked pumpkin protein muffins sits on a countertop, surrounded by chocolate chips, an empty muffin liner, a bowl of pumpkin puree, and a bottle of milk.

Cool and serve. After the muffins cool a little bit in the pan (about 5 minutes), move them to a wire rack to cool the rest of the way. Enjoy!

Erin’s Tip

I like using a large cookie scoop to portion the batter so all of the muffins are roughly the same size and bake evenly.

Pumpkin protein muffins on a white surface, with a glass jar labeled Pumpkin Pie Spice, an empty muffin liner, and a glass of milk in the background.

More Gluten-Free Protein-Packed Breakfast Recipes

A wicker basket filled with pumpkin protein muffins topped with chocolate chips, with a small bowl of chocolate chips nearby.
5 from 7 votes

Gluten-Free Pumpkin Protein Muffins

Author Erin Collins
Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Servings 24 muffins
I love the bakery-style gluten-free pumpkin muffins on my website, but I wanted to create a healthier, protein-packed version for my teenage athlete.
These muffins are soft, perfectly spiced and a hit with my whole family! They have about 6 grams of protein per muffin and are made with a whole can of pumpkin. I love keeping some in the freezer for busy mornings or after-practice snacks.
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Ingredients

Dry Ingredients

Other Ingredients

  • One 15-ounce can (425g) pumpkin purée
  • 1½ cups (360g) plain Greek yogurt
  • 4 large eggs
  • ¼ cup maple syrup
  • 1 teaspoon vanilla extract
  • 1 cup (170g) semi-sweet chocolate chips

Instructions 

  • Preheat the oven to 350°F. Line two standard muffin pans with paper baking cups.
  • In a large bowl, whisk together the gluten-free flour, protein powder, coconut sugar, baking powder, baking soda, salt, cinnamon and pumpkin pie spice.
  • In a medium bowl, whisk together the pumpkin purée, Greek yogurt, eggs, maple syrup and vanilla extract until smooth.
  • Add the pumpkin mixture to the dry ingredients and stir with a rubber spatula until just combined and no dry flour streaks remain. Fold in the chocolate chips.
  • Using a kitchen scoop or large spoon, portion the batter evenly into the prepared muffin pans.
  • Bake for 25 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  • Let the muffins cool in the pans for 5 minutes, then transfer to a wire rack to cool completely.

Notes

Gluten-Free: Use a high-quality gluten-free measure-for-measure flour that contains xanthan gum and a certified gluten-free protein powder.
Dairy-Free: Since this recipe uses so much yogurt for structure, these muffins won’t work with dairy-free substitutions.
Make-Ahead: The baked muffins keep well for an easy make-ahead recipe! I don’t recommend making the batter ahead of time and refrigerating since it contains baking powder and soda.
To Store: Store in an airtight container at room temperature for up to 3 days for best texture. You can also refrigerate them for up to 5 days. I like to let them come to room temperature before eating.
To Freeze: Freeze cooled muffins for up to 3 months. I love wrapping them individually so that I can easily thaw one or two when I need them. Thaw at room temperature for about 1-2 hours.

Nutrition

Calories: 139kcal | Carbohydrates: 20g | Protein: 7g | Fat: 4g | Saturated Fat: 2g | Polyunsaturated Fat: 0.3g | Monounsaturated Fat: 1g | Trans Fat: 0.01g | Cholesterol: 38mg | Sodium: 132mg | Potassium: 131mg | Fiber: 2g | Sugar: 9g | Vitamin A: 45IU | Vitamin C: 0.03mg | Calcium: 73mg | Iron: 1mg

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Hi, I'm Erin!

BS Food Science,

MS Nutrition

I believe you can make amazing, gluten-free food with everyday ingredients that everyone will enjoy. I'm here to share my tried-and-true recipes with you!

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Comments

    1. Hi Cindy! The Greek yogurt plays a big role in these muffins so we wouldn’t recommend using cottage cheese instead. It has a different consistency and moisture level so it would most likely change the texture too much. Thank you for your question!

      Reply

  2. 5 stars
    Wanted to make something “pumpkiny” today! Found this recipe on your site and was happy to make something a little healthier as well! Very fluffy and quite tasty! Mine stuck a little to the wrapper…not sure why but very delicious!!

    Reply

    1. We’re so happy to hear you loved the flavor and texture of these new muffins! Thank you for the wonderful feedback, Christy. We like to use these paper liners to prevent sticking. We hope your next batch is just as enjoyable and sticks less! Happy baking!

      Reply

  3. 5 stars
    I just wanted to say these are amazing! We are a DF house so I used a Vanilla Good Protein and Silk Vanilla Greek yogurt. Everything else, I kept the same. They turned out amazing!

    Reply

    1. We’re so happy to hear the dairy-free substitutions worked well for you, Simonne! Thanks for sharing with us. We’re so glad you loved the new muffin recipe!

      Reply

  4. I am so excited to try these!! Will an egg replacer, such as bob’s red mill work here? I am hoping to make these for a family get together, and we have an egg allergy.

    Reply

  5. 5 stars
    I baked these delicious muffins up yesterday. I like that the recipe makes 24 muffins, enough for sharing around. The only substitution I had to make was with the sugar. I did not have coconut sugar on hand, so I used turbinado sugar. It did not seem to affect the outcome. This is a great recipe, and I love the fact that each muffin has 6 grams of protein!! Great for the morning with my coffee. Thank you!

    Reply

    1. Yay! We’re thrilled to hear you enjoyed the new pumpkin protein muffins. It’s great to hear the turbinado sugar worked well as a sub. Thank you for sharing this with us, Mindy. Happy baking!

      Reply

  6. Hi Christie, Can I use Coconut greek yogurt. I like to use coco june or forager. I would like to try making these but prefer non dairy yogurt, I will wait for your reply before I try making them. Thanks.

    Reply

    1. Hi Mark! We don’t recommend dairy-free substitutes for these muffins since the recipe uses so much Greek yogurt for structure. Thank you for your question! Happy baking!

      Reply

  7. 5 stars
    Really liked this practical recipe. I had a few pecans on hand and they were delicious. This is basic and yet very versatile. Great fall recipe!! This is a “keeper” for me.

    Reply

    1. We’re so happy to hear you enjoyed the recipe enough to consider it a keeper, Stephani! Thank you for sharing your positive baking experience with us!

      Reply

    1. Yay! We love to hear when our recipes become new family favorites. Thank you for the amazing feedback, Sarah!

      Reply

  9. 5 stars
    We love these muffins. They are moist and delicious. I only had mini chocolate chips, so I used those and they were still very good. Next time I will use the larger chips. Love the extra punch of protein.

    Reply

    1. We’re thrilled to hear you enjoyed the new pumpkin muffin recipe, Donna! Thank you for sharing how it went with the mini chips. We hope you love them just as much with the larger chocolate chips next time! Happy baking!

      Reply

        1. Hi Becky! Yes, you’ll use the same amount of brown sugar as you would coconut sugar. We hope you love the muffins!

          Reply

    1. Hi Megan! If not wanting to use protein powder, we’d recommend our classic gluten-free pumpkin muffin recipe instead. The ingredients in this protein muffin version are specifically balanced for the protein powder so flour won’t work as a 1:1 swap. We hope this helps! Happy baking!

      Reply
5 from 7 votes

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