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Chocolate Chip Protein Cookie Recipe (Gluten free)

This healthy butternut squash chocolate chip protein cookie recipe is the perfect sweet snack. These chocolate chip protein cookies are packed with fiber and protein, this easy recipe is gluten free, vegan and only needs one bowl and a spoon to make!

White plate stacked with 4 butternut squash chocolate chip protein cookies with chocolate chips around the plate

This recipe started from my need to use up half of a can of butternut squash puree after using the rest for a different recipe. I had been working on a pumpkin cookie recipe, but this butternut squash added just a bit of sweetness that the pumpkin cookies were missing.

If you like a moist, dense subtly sweet cookie, you are going to love this recipe for healthy butternut squash chocolate chip protein cookies. These cookies are perfect for post workout snacks or could even be eaten for breakfast with a little almond butter or pumpkin sunbutter on top.

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How to make chocolate chip protein cookies

My tip to make the best gluten free protein cookies is to use a vegan protein powder. The protein powder replaces the flour in a typical cookie recipe. Vegan protein powder absorbs water and acts just like flour. However whey protein, egg protein or collagen peptides do not absorb liquid like vegan protein powder, so I don’t recommend using those in place of the vegan protein powder.

I highly recommend Nuzest protein powder. It’s tested for heavy metals and does not have any added sugars or artificial sweeteners or artificial flavors. This is the only protein powder I bake with and I recommend it to everyone!  

Black wire cooling rack filled with butternut squash chocolate chip protein cookies

Tips for making the best protein cookies:

Use the best ingredients!

This recipe uses tigernut flour to keep it grain free and gluten free. I love using tigernut flour because it’s a great source of healthy fiber, it’s a prebiotic (which means it’s good for your gut and digestion) and it’s easy to digest! If you don’t have tigernut flour, you could substitute your favorite gluten free flour or almond flour. You could also use 2-3 tbsp of coconut flour as well.

Use a high quality dairy free chocolate chip. I love the 85% dark chocolate Pascha Brand chocolate chips.  They are low in sugar and are the perfect amount of sweetness. I also enjoy the dark chocolate morsels from Enjoy Life Brands.

Metal basket filled with butternut squash chocolate chip protein cookie recipe with a white cookie jar in the background

Make the cookies all the same size

Use a cookie scoop or a tablespoon to measure the cookies out to be the same size. This ensures that the cookies all bake at the same time! I used 2 tablespoons of batter for each cookie so that the butternut squash chocolate chip protein cookies were a good sized snack! These cookies are so dense and filling, they are the perfect afternoon snack or late night treat!

Have fun with the filling!

You can add cacao nibs, chopped pecans, chopped walnuts, pumpkin seeds, sunflower seeds, dried cranberries, raisins or whatever your favorite cookie add-in might be.

You can also use ground cinnamon or pumpkin pie spice blend for a fun way to change things up.

Healthy butternut squash chocolate chip protein cookies lined up on a black wire baking rack.

Allow the cookies to cool completely

One thing I have learned with baking with protein powder is that the recipe always tastes better when it has cooled completely. These butternut squash chocolate chip cookies are actually the best when they are refrigerated, so if you can make them ahead of time, I highly recommend it!

How to store these butternut squash chocolate chip protein cookies:

These gluten free chocolate chip protein cookies are best stored in the refrigerator, for up to a week in a tightly sealed pyrex or ziplock bag. You can also store these cookies in the freezer in a freezer bag (which is actually my favorite way to enjoy them).

Overhead shot of a silver basket filled with butternut squash chocolate chip protein cookies with a white napkin in the front of the basket

To make this recipe for butternut squash chocolate chip protein cookies egg free, I used ground flax seeds. You could also use chia seeds if you don’t have ground flax seeds.

To make this recipe vegan, you will need to make sure you use a vegan protein powder and a dairy free chocolate chip as well.

★ Did you make this recipe? Please give it a star rating below!
White plate with healthy butternut squash chocolate chip protein cookie recipe stacked in a pile with a basket of cookies in the background

Healthy Butternut Squash Chocolate Chip Protein Cookie Recipe

This healthy butternut squash chocolate chip protein cookie recipe is an easy dessert recipe that is filled with fiber and protein and is the perfect treat for clean eating! These gluten free vegan cookies are egg free and dairy free and are the perfect afternoon snack or breakfast recipe. 
5 from 1 vote
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Course: Dessert
Cuisine: American
Keyword: butternut squash protein cookies, chocolate chip protein cookies, vegan protein cookies
Prep Time: 7 minutes
Cook Time: 21 minutes
Total Time: 28 minutes
Servings: 28 cookies

Guided Recipe Video


  • Preheat the oven to 350F
  • In a large bowl, mash the bananas. Add the can of butternut squash puree and water. Stir well
  • Add the ground flax seeds to the liquid mixture. 
  • Add the protein powder and tigernut flour to the wet mixture and stir well. 
  • Add the pumpkin pie seasoning, cinnamon, vanilla extract, baking powder, baking soda, apple cider vinegar and salt to the mixture and stir well.
  • Stir in the chocolate chips
  • Use a silicone mat or parchment paper on a baking sheet. Spray with non-stick spray. Using a tablespoon, measure out 2 tablespoons per cookie.
  • Each baking sheet can hold about 20 cookies. 
  • Bake at 350F for 21 minutes. 
  • Allow to cool completely. Best if refrigerated. 
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Nutrition Information

Nutrition Facts
Amount per Serving
Where does nutrition info come from? Nutrition facts are provided as a courtesy, sourced from the USDA Food Database.
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Recipe Rating


Monday 20th of January 2020

Sounds delicious...I would like to make it with eggs would I do that?

Samantha Rowland

Tuesday 21st of January 2020

Hey there Diane. I have not made this recipe without eggs. I would suggest you look for a egg free recipe to get the best results! Best of luck!


Tuesday 13th of November 2018

Pretty sure this is the moistest cookie I've ever made! A keeper for sure.