Recipe: Gut Healthy Butternut Squash Protein Cookies (Paleo, SCD, GAPS)

Recipe: Gut Healthy Butternut Squash Protein Cookies (Paleo, SCD, GAPS) post image

I usually have an abundance of winter squash already cooked in my refrigerator. Sometimes I have so much I have to come up with a way to use it up. Here is a fantastic cookie that is totally healthy!

I love using collagen peptides (from grassfed cows) in everything I bake now, because it adds protein peptides that are critical to good health in general, and great, in particular, for your gut lining, joint cartilage and skin. The protein also offsets the carbohydrate content of this recipe, making it a more balanced treat.

Collagen for Gut Health

Collagen tissue makes up 50% of the protein in the body, as it is the primary protein in connective tissue – the tissue that makes up fibrous tissues like tendons, ligaments, bone, cartilage and skin. Collagen makes up the matrix of joint cartilage and skin as well as cornea of the eye, bone, blood vessels, the gut lining, and intervertebral discs.

Collagen peptides come from gelatin which is composed mainly of the amino acids glycine, proline and hydroxyproline. These amino acids are critical to healthy matrix structures as outlined above. Gelatin protein can be used to make homemade jello, gummies or used as a thickener in puddings because it gels.

Collagen Peptides are derived from gelatin, and contain the same amino acids as gelatin. The main difference is that these are further processed by using an enzyme to add water molecules so that it can dissolve instantly in hot or cold liquids without gelling. This is great for baking, soups, gravies and shakes!

This is a healthy cookie to begin with and the collagen peptides make it even healthier!

Here is the easiest way to make winter squash!

Nutrition in Butternut Squash

Butternut squash is super high in vitamin A and also contains vitamin C, folate and a small amount of vitamins K and E. There are also minerals such as, magnesium, phosphorus, potassium and calcium.

There is also a very nice omega 3 to 6 profile of 2 to 1.

Having been on the SCD and GAPS diets for a few years, I always have some in the refrigerator or freezer, as I use it for so many things. Winter squash blends well into soups and gravies and it adds moisture and substance to grain free muffins and breads, cakes and cookies.

I think you will love this recipe!

Butternut Squash Protein Cookies

Prep Time: 10 minutes

Cook Time: 25 minutes

Yield: 60 - 70 cookies depending on size



  1. Preheat the oven to 325º F and prepare 3 cookies sheets with parchment paper
  2. In a food processor, process the butternut squash until smooth
  3. Add the eggs, virgin coconut oil and maple sweetener (or honey) and mix
  4. Add the collagen peptides, coconut flour, salt, baking soda and spices and mix
  5. Add the raisins and mix well - I like very small pieces of raisins
  6. Place the batter into a bowl for ease
  7. Place a teaspoon of the batter onto the parchment paper and press down lightly on the batter with your other hand
  8. Fill the cookie sheets this way
  9. Bake for 20 to 25 minutes until lightly browned on top
  10. Cool on the baking sheet for a few minutes then on a rack
  11. These freeze well


Like this recipe? Get many more and tons of information and instructions on using grain free flours in my fantastic kindle books. You don’t need a kindle to read them, as Amazon offers a FREE reader for all devices, on the sales page for each book.

Grab my kindle books here!
Grain Free Paleo Breads
Grain Free Paleo Snacks
Grain Free Paleo Desserts and Treats

These recipes are suitable for Paleo, SCD, GAPS and all grain free eaters.


















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Tropical Traditions Gold Label Virgin Coconut Oil

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Leave a Comment

  • Liz A March 27, 2017, 1:50 pm

    This sounds great! Can I make it using gelatin, do you think? Maybe with some adaptations?


    • Dr. Jill March 27, 2017, 4:02 pm

      Hi Liz,
      You could use actually use gelatin in place of some of the eggs – you would have to bloom it first in some water. I’m not sure how it would hold together though as a cookie…

      • Liz A March 28, 2017, 10:53 pm

        Oh, thank you. But I’m sorry, I meant can I use gelatin instead of collagen peptides? I just spent a lot on the grass-fed gelatin, so I can’t get the peptides, too. 🙂

        • Dr. Jill April 3, 2017, 4:36 pm

          Yes as explained above and still use the eggs. You still have to “bloom” the gelatin.

  • custom thesis writing June 21, 2017, 2:15 am

    Hello! Thanks so much for the directions! Actually, I don’t know a parchment paper, but at least I know where to buy it!