Skip to content

A Holistic Nutritionist’s Favorite Chocolate Chip Cookie Recipe

This classic chocolate chip cookie recipe makes cookies so chewy and full of nostalgia. They are made easily digestible and mineral-rich with sprouted whole wheat flour, mineral-rich sugar, black strap molasses, and other nutrient-dense ingredients.

The chocolate chip cookie is a childhood staple food. I remember eating them frequently after being chopped from the refrigerated yellow log and baked into chewy goodness. My days with the infamous yellow log are long gone, but I still enjoy a good chocolate chip cookie with better quality ingredients.

These cookies are so easy, relatively quick to make, and the ingredients are up to my standards as a Nutritional Therapy Practitioner. I would happily feed these to my children, and I do! This is by far our favorite cookie recipe.

A Holistic Nutritionist's Favorite Chocolate Chip Cookie Recipe | Nutritional Therapy | How to Nourish | @howtonourish
Breaking Down the Ingredients
  • Unsalted organic grass-fed butter. A high-quality butter like organic grass-fed is a healthy source of rich saturated fat, as well as important vitamins A, D, and K2. Grass is a cow’s natural diet and improves the nutrient profile of butter. Skip the salted butter to better control the flavor of your cookies.
  • Panela cane sugar, coconut sugar, or maple sugar. Processed cane sugar is stripped of minerals, making it a burden for the body to digest as it pulls minerals from the body. These three sugars are different in that it they are minimally processed, which allows them to retain their beautiful nutrient profiles. Panela sugar is rich in calcium, iron, magnesium, manganese, phosphorus, potassium, and zinc. Coconut sugar and maple sugar are also more rich in minerals than white cane sugar.
  • Black strap molasses. Molasses gives cookies a rich chewy flavor and texture, and black strap molasses specifically is rich in calcium, iron, potassium, and vitamin A.
  • Eggs. Rich in saturated fat, vitamins, and minerals. Whole eggs really are a perfect food.
  • Organic vanilla extract. For that classic chocolate cookie flavor.
  • Organic sprouted whole wheat flour. Wheat flour contains gluten proteins that are notoriously difficult to digest. Sprouting wheat before it is made into flour improves the digestibility of gluten proteins significantly, breaks down harmful oxalates, and makes wheat’s many nutrients much more bioavailable. Sprouted wheat is a good source of iron, potassium, magnesium, zinc, phosphorus, copper, manganese, selenium, and vitamin E.
  • Baking soda. To help fluff them up.
  • Coarse sea salt. A great way to add in extra trace minerals and give the cookies a bit of salty crunch.
  • Mini semi-sweet chocolate chips. Mini chips are so fun, but you can use anything you have on hand.
A Holistic Nutritionist's Favorite Chocolate Chip Cookie Recipe | Nutritional Therapy | How to Nourish | @howtonourish
Questions & Answers

Can I eat this cookie dough raw?
This recipe uses milled flour and raw eggs which, depending on your sourcing, may contain harmful bacteria that won’t sit well in your digestive tract. Because I can’t personally guarantee your ingredients, I would say no, please don’t eat it raw.

Can I use white cane sugar or maple syrup in place of the recommended granulated sugars?
Most granulated sweeteners can substitute 1:1 with the options I included, however they will not add as many minerals to your cookies as the panela cane sugar, coconut sugar, or maple sugar will. Liquid sweeteners will likely make your dough too loose, so I would recommend sticking with granulated sweeteners in this recipe.

Can I use gluten-free flour in place of the sprouted wheat flour?
You can substitute a 1:1 gluten free flour blend, but I have not tested this recipe with gluten free flour so I can’t tell you if it still retains the same qualities that make this chocolate chip cookie recipe so scrumptious.

Can I use different chocolate chips or chunks instead of mini chips?
Yes! That should work out well. You may need to use more to fill out the cookies well, as the density of larger chips or chunks will be different than mini chips in a 1-cup measuring cup.

A Holistic Nutritionist’s Favorite Chocolate Chip Cookie Recipe

Recipe by Heather Hart


Prep Time


Bake Time


Total Time




  • 3/4 cup unsalted organic grass-fed butter

  • 1 1/4 cup panela cane sugar, coconut sugar, or maple sugar

  • 1 tablespoon black strap molasses

  • 1 egg yolk + 1 whole egg, set out until room temperature

  • 1 tablespoon vanilla extract

  • 1 3/4 cup sprouted whole wheat flour

  • 3/4 teaspoon baking soda

  • 1 teaspoon coarse sea salt

  • 1 cup mini semi-sweet chocolate chips


  • Add butter to a small saucepan over medium heat. Stir constantly until it begins to foam and turn a light golden brown. As soon as you get to this stage, remove the saucepan from heat and let it cool for 10-15 minutes.
  • In a large mixing bowl, combine the brown butter, sugar, and molasses. Whisk well until mixed. Add in the egg and yolk, and vanilla extract. Whisk thoroughly until it starts to fluff just a bit.
  • In a separate small mixing bowl, stir together the flour, baking soda, and salt.
  • Add half the dry ingredients into the wet ingredients and whisk until well combined. Pour half of the leftover dry ingredients and mix again, then continue pouring just a bit until it has all been added in. Fold in the chocolate chips, taking care to mix just enough to incorporate the ingredients.
  • Place a lid or wet towel over the bowl and refrigerate for 30-60 minutes, or longer if you would like to make the dough ahead of time*.
  • When ready to bake, preheat your oven to 350ºF. Line a baking sheet with parchment paper.
  • Using a spoon or just your hands, form 1.5 inch balls of dough and place them on the baking sheet with at least one inch between them. Bake for 11 minutes, checking at 9 minutes for doneness. Edges should be lightly golden brown and centers should be puffed and still slightly undercooked.
  • Allow cookies to cool at least 5 minutes before eating. Enjoy with a glass of raw milk!


  • *Refrigerate unbaked dough for up to 24 hours to make ahead of time. Begin with Step 6 when ready to bake.
  • Baked cookies should keep in a closed container on the counter for a few days, or in the fridge for a week or longer. I have not tried freezing them, but I imagine they would freeze well. Reheat on a baking sheet in a low-heat oven until just warm.

Are you making this recipe? Please consider sharing and tag @howtonourish on Instagram!

To learn more about nutritional therapy, please feel free to browse my other blog posts here.

Leave a Reply

Your email address will not be published. Required fields are marked *