Healthy Gut Nut-Flour-Free Chocolate Chip Cookies

nut and flour free chocolate chip cookies

There’s nothing else like it… warm, gooey, chocolate chip cookies fresh from the oven.

(Hey, there’s nothing wrong with wanting to enjoy a cookie sometimes! After all, delicious food is one of life’s greatest pleasures.)

Even if you’re following a healthy gut, grain-free diet like SCD or paleo, you shouldn’t have to give up the occasional cookie.

But here’s the problem: a lot of gut-healthy, grain-free recipes rely way too much on one ingredient that may be holding you back from healing: nut flour.

The Problem With Nut Flours

Most grain-free baking recipes use nut flours like almond as a replacement for traditional wheat flour or gluten-free flours like rice.

But, nut flours can be really difficult for those with a compromised gut to digest. They cause issues for so many people that we call nuts one of the “4 Horsemen of SCD.”

Nut flours are also high in Omega-6 fats. For optimal health, Omega-3 and -6 fats need to be balanced in the body. If you’re eating lots of fats rich in Omega-3, like wild-caught fish, this may not be a problem for you. But most people eat far more Omega-6 than they do Omega-3.

(For more on healthy fats, check this out.)

If you’ve tried other grain-free baked goods and not tolerated them well, it could be because of nut flours. And if you’re eating a lot of nut flour and not seeing progress in healing your gut, you may want to consider cutting back on it.

Enter Coconut Flour

Coconut flour is my favorite nut-free, grain-free flour to bake with. It’s gluten-free, grain-free and well-tolerated by most people.

If you don’t tolerate nut-flour, or just want to stop eating so much nut flour, coconut flour might be your new go-to.

Coconut flour is very absorbent, though – it’s like a sponge and will suck up lots of liquid. For this reason, coconut flour has developed a reputation as being hard to work with and dry.

While it’s true that a nut-flour baked good is usually more moist than a coconut-flour baked good, you can still make a great cookie with coconut flour (I have eaten LOTS of cookies that prove it!).

Trust your intuition when you’re baking with coconut flour – if your cookie dough is too dry, you can always thin it with a little more liquid or fat.

Let’s Talk About Chocolate

At SCD Lifestyle, we are all about finding the customized diet that works for you.

That means some members of our community eat chocolate, while others avoid it.

If you’re strictly following the Specific Carbohydrate Diet, chocolate is considered illegal. (Carob is illegal on SCD, too – but it may be OK if you’re following AIP or another gut healing diet.)

If you’re including chocolate, choose a high-quality dark or semi-sweet chocolate. I use Enjoy Life allergen-friendly chocolate chips.

For those who avoid chocolate, some other options are dried fruit like raisins, unsweetened flake coconut, or carob chips. If you do tolerate nuts, you could also add some chopped nuts to the dough.

Or, you can do like I sometimes do and add a little extra cinnamon and skip the chips altogether!

Remember, you’re the boss of your own diet. Make substitutions as you need to to suit your own body. I’ve included substitutes and suggestions in the recipe as a starting point.

(Are you stuck on a restricted diet, unable to introduce more foods? That can be a sign of leaky gut.)

One For Me Now, One For Me Later

As with ANY food, cookies – even healthy gut cookies – should be eaten in moderation. Plus, these cookies are best fresh from the oven. That’s why I recommend portioning and freezing the dough.

Once dough is assembled, scoop into balls (forming round balls with your hand will result in the prettiest cookies). Freeze on cookie sheet for 30 minutes, then transfer frozen dough balls to an airtight container and keep frozen for a hot, fresh cookie anytime.

This healthy gut cookie recipe is the one I use when I’ve got a cookie craving. Whether you want to experience the joy of baking with your kids, or just want a special afternoon snack, I hope you enjoy it.

Healthy Gut Nut-Flour-Free Chocolate Chip Cookies


  • ½ cup coconut flour
  • ¼ tsp baking soda
  • ¼ tsp salt
  • ½ tsp cinnamon (more to taste)
  • 1 tsp vanilla extract (gluten free)
  • 1/3 cup coconut sugar OR maple syrup (your preference)
  • 3 eggs
  • 1/3 cup coconut oil or high-quality butter, melted
  • ½ cup chocolate chips, coconut, raisins, or other add-in


Combine coconut flour, baking soda, salt, cinnamon, and coconut sugar (if using – if using maple syrup, add it with the other wet ingredients) in a medium bowl. Mix to incorporate. Then, add wet ingredients and stir to form a dough. Add chocolate chips or other mix-in and stir to combine.

Form dough into medium-size balls (like a ping-pong ball). Freeze or bake immediately.

To bake, preheat oven to 350°F and bake for 12-16 minutes, or until bottom of cookie is golden brown. Let cool for 10 minutes before eating.

P.S. Did you try this recipe? Leave us a comment and tell us how it turned out for you.

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