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  • Writer's pictureGutsy Baker

The Best Paleo Chocolate Chip Cookies (Gluten Free, Dairy Free)

If you follow me on Instagram, you know I've been trying for weeks and weeks to convert my browned butter gluten free chocolate chip cookies into a paleo version. This means swapping out the gluten free flour blend for paleo flours. It was not easy! Paleo flours do not absorb moisture the way gluten free flours do, so I had to end up doubling the flour content and switching around the flours a total of 9 times! yes, 9 attempts. But they came out perfect in the end and they taste like a chewy chocolate chip cookie from a bakery!


If you love cookies, and you are paleo or eat low carb and craving a classic chocolate chip cookie, these cookies will satisfy that craving! I have made these cookies for my diabetic aunt and have had requests at a local store in my family's town to package and sell them! If you are looking for a paleo dessert or a gluten free dessert, these cookies are the perfect chocolate fix. They're even safe for a low fodmap diet.

My dad refuses to eat anything labeled 'gluten free' and he's been telling everyone how 'real' these cookies are! They ARE. THE. BEST. And if you can't eat nuts, use this recipe! It's almost the same but the flours are different.

These chewy chocolate chip cookies are paleo, grain free, dairy free and low fodmap!

And somehow they magically taste like they came from a bakery! They're made with a combination of almond flour, tapioca starch and coconut flour, sweetened lightly with coconut sugar and a smidge of molasses to create a brown sugar. This gives you the texture of a real chocolate chip cookie.

The secret ingredient in the best paleo chocolate chip cookies:

These chocolate chip cookies are full of flavor, sweet & salty and have that iconic chocolate chip cookie taste that you’d get at a bakery. Using blackstrap molasses is the secret to achieving that iconic cookie texture and flavor, while keeping them paleo! Brown sugar is what typically makes chocolate chip cookies chewy. But brown sugar is still refined, and is not paleo friendly. My secret to making a paleo brown sugar is adding a touch of blackstrap molasses to coconut sugar. Molasses is found in traditional brown sugar, and adding a touch into the coconut sugar gives them the perfect soft brown sugar texture and the perfect taste and chew!

What is blackstrap molasses?

Blackstrap molasses is a specific type of molasses that is very high in iron and minerals. It's actually considered a superfood, but is also lower in sugar than regular molasses. I prefer its rich flavor. In this recipe, 1 1/2 teaspoons of blackstrap molasses is added to the coconut sugar to create a paleo-friendly brown sugar substitute.

What do I need for these paleo chewy chocolate chip cookies?

  • A baking sheet

  • A preferred cookie scoop for even, perfect cookies

  • A hand mixer

Are these chocolate chip cookies easy to make?

Easy level baking! Once the dough is mixed by hand and chilled, it's just scoop, press down and bake!

How to store paleo chocolate chip cookies:

Store on a vented dish, platter or in a container on the counter for up to 2 days, then transfer to the fridge in an airtight container for up to 7. Storing in an airtight container will make these cookies softer.

What is in these paleo chocolate chip cookies?

Almond Flour: I use almond flour in these cookies for moisture or to keep them low carb

Tapioca Starch: This helps bind the cookies together and works with the almond flour. Arrowroot can be subbed

Coconut Flour: Coconut flour helps absorb moisture in baking, this can't be subbed!

Coconut Sugar: This is my go-to for sweetening all my baked goods. It’s a neutral flavor and low glycemic so works well on low sugar diets. I combined the coconut sugar in this recipe with a touch of molasses to substitute brown sugar and it worked perfectly

Blackstrap Molasses: Just a touch of molasses in these cookies to create a brown sugar substitute. This is what gives your cookies a chewy texture. Blackstrap molasses is rich in iron and minerals and actually a superfood!

Baking soda: This is what makes your cookies spread and gives them a little ris

Sea salt: A touch of sea salt to balance out the sweetness

Non Dairy Butter: I used Miyoko’s butter here, but any vegan stick butter should work, or regular grass fed butter

Eggs: This recipe calls for one egg and one egg yolk, which also helps with the chewiness. I have not tried any substitutes here but 2 aquafaba eggs may work.

Vanilla Extract: Because we put this in all baked goods, am I right?

Chocolate Chips: I love to use paleo chocolate chips here, Hu Kitchen is my weapon of choice


  • 1 1/2 cups fine almond flour

  • 1 1/2 cups tapioca starch

  • 6 tbsp coconut flour

  • 1/2 tsp baking soda

  • 1/2 tsp sea salt

  • 1 cup coconut sugar

  • 1 1/2 tsp blackstrap molasses (any molasses will work)

  • 1 egg + 1 egg yolk

  • 1 tbsp of vanilla extract

  • 3/4 cup of unsalted non-dairy butter or grass fed butter (I've used Miyoko’s and Earth Balance Unsalted Sticks)

  • 1 cup of chocolate chunks or chips, I use Hu Kitchen

Make the cookies:

1. Preheat the oven to 350F and line a large baking sheet with parchment paper. Set aside.

2. In a medium bowl, mix together the coconut sugar and the molasses. Crumble together, it will start to resemble a traditional soft brown sugar texture. Add in softened butter and mix with a hand mixer until it becomes creamed, about 1-2 minutes. Now fold in egg and egg yolk and mix again until just combined. Finally add in your vanilla extract and mix until just combined. Try not to overmix.

3. In another medium bowl, combine your flours/starch, sea salt, baking soda and mix well.

4. Carefully combine the dry into the wet ingredients and mix for a full minute or more by hand until smooth dough forms, the coconut sugar granules should not be visible. The dough may be a little sticky and not totally scoopable yet, this is normal.

5. Add in the chocolate chips, putting few aside to add on top later. Cover the bowl with plastic and place in the fridge for at least 30-45 minutes to chill. Can be up to overnight. The dough will become solid and scoopable once chilled.

6. Once dough is chilled, preheat your oven to 350F. Line a large baking sheet with parchment paper. Use a cookie scooper or a large spoon and scoop out the dough in balls and place them onto lined sheet. The balls should be about 1 1/2" round, or roughly 1 1/2 tbsp of dough. Press down the balls with your fingers just so the tops flatten, and they are approx 1/2" thick discs.

7. Repeat scooping and placing on the cookie sheet until all dough is used. Place the extra chocolate chips on top and sprinkle with flaky sea salt. Bake for 10-12 minutes until edges are JUST set and the inside is still a bit undercooked. This is how you get a nice chewy center.

8. Transfer cookies from the baking sheet to a cooling rack and let cool completely. Store in an airtight container on the counter for 3 days, and then transfer to the fridge for another 7 days. These store well in the freezer, too.

9. Enjoy with a tall glass of dairy free milk!!


  • Take your cookies out of the oven as soon as the edges set, about 10-12 minutes. If you use a larger scoop for your cookies they make take 1-2 minutes longer. But taking the cookies out a bit underbaked will give them the perfect chewy gooey texture.

  • I haven't tried a substitution for the eggs in this recipe but I think the best vegan sub would be aquafaba (4 tbsp of chickpea water). If you try this, let me know in the comments how it turned out. Flax eggs may work as well but the cookies could be a little more dense and less soft.

If you make these delicious paleo chocolate chip cookies, leave me comments or ratings below! And as always, tag me @gutsy_baker on Instagram, I love to see your creations!

xo Stephanie


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