Healthy Gut Nut-Flour-Free Chocolate Chip Cookies

by Steven Wright

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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About the author

Steven Wright Steve Wright is a health engineer and author. In 2009, he reached a breaking point when IBS took over his life and the doctors didn't know how to help. Since then, he has transformed his health and started to help others naturally heal stomach problems. You can check out his story here and find him on Google+, Facebook or Twitter.

The Specific Carbohydrate Diet Works

{ 17 comments… read them below or add one }

Olive Jason March 22, 2018 at 3:50 am

this is interesting gonna try them out

SUSAN JOHNSON March 8, 2018 at 1:47 pm

I am recent to SCD and am dying for something sweet. I thought that coconut sugar and maple syrup were on the illegal list so I’m confused on this recipe.

Mariel Heiss March 9, 2018 at 10:20 am

Hi Susan – like we mentioned, if you’re following very strict SCD, this recipe isn’t for you without some modification. To make it work for you, substitute the maple syrup for honey and omit the chocolate chips.

Denese February 27, 2018 at 1:24 pm

Tried this recipe. I thought the quantity of chocolate chips was a bit much for the amount of dough. And although I was able to shape the first few into round-ish balls, then the dough began to stick to my hands and it became difficult to shape the last half. Perhaps a dish of water or a bit of oil nearby would help. I hadn’t used it before but I guess the coconut flour is super absorbent. I thought they wouldn’t hold together. But they did, and we really enjoyed them. I should have put the oven rack up higher — I’ll do that next time.

Mariel Heiss February 28, 2018 at 12:25 pm

Thanks for your feedback Denese, and glad you enjoyed the cookies 🙂

The amount of chocolate chips sued is a very personal decision 😉 It won’t mess up the recipe to use more or less to your preference – when I make these, I jsut eyeball the amount.

For scooping the dough, I use either 2 spoons (one to scoop it, one to scrape it) or a cookie scoop that is spring loaded. If you’re using your hands, spraying them with a bit of coconut oil before starting can really help!

Makhatran February 25, 2018 at 4:49 pm

I have a problem with coconut, both flour and fat, probably a FODMAP thing. Is there any way to bake these cookies with something else than nut and coconut?

Mariel Heiss February 26, 2018 at 10:36 am

Hi Makhatran – I can’t recommend any 1-1- substitute for coconut flour in this recipe, because coconut flour is much more absorbent than other alternative flours, so the other ingredients would have to be adjusted as well. Sorry about that!

Anna Weisman February 27, 2018 at 11:10 pm

Try finding a recipe with starchy veggie flour like cassava or tiger nut

Donna Yokiel February 24, 2018 at 6:06 pm

Like the recipe. I’m not on any special diet, but try to eat grain free, simply because I’ve found I feel better. So I’m always looking for these types of recipes. Thanks!

Rosa February 24, 2018 at 2:43 pm

I see that coconut in all its versions (flour, sugar and oil), is recomended for this and many more recipes. But, I have a question, in some cases, when the LCL cholesterol is high, the use of coconut is a good option?

Mariel Heiss February 26, 2018 at 10:38 am

Hi Rosa – the idea that eating healthy foods high in saturated fats (like coconut or eggs) raises cholesterol has been pretty well debunked!! Heres a great article explaining this myth:

Adrienne Lawrence February 24, 2018 at 1:11 pm

Can you tell me what the macro nutrients are? Can you substitute Swerve or liquid Stevia and if so, how much should be added? Thanks! Chocolate chip cookies! Yum!

Mariel Heiss February 26, 2018 at 10:40 am

Hi Adrienne – you could calculate the macros by placing all the ingredients in a calorie calculator. As for replacing the sweetener – we don’t recommend any artificial sweeteners or stevia. You could always try it – but you might have to experiment a few times to get the sweetness right (and we’re not sure how it would affect the texture).

T Leckie February 23, 2018 at 9:25 am

Maybe I missed something but these cookies contain sweetener other than honey (husband is on SCD and we are being DILIGENT with his food!). Can you comment on this aspect please? Thanks!

Mariel Heiss February 23, 2018 at 11:51 am

Yes – these cookies aren’t going to be “SCD Legal” if you strictly follow SCD (because they also contain chocolate!!)

But – you could definitely substitute honey for the maple syrup (equal amount) and either omit the chocolate or substitute raisins, etc.

Tammy February 23, 2018 at 7:32 am

As I scrolled and read I got more excited about making these cookies. You seemed to be covering all the allergen/sensitive food issues (nuts-no nuts, chocolate-no chocolate, etc) and giving alternatives. By the time I got to the actual recipe I was sure I’d have no problem, and then bam, eggs! I was so surprised that you hadn’t addressed that above the recipe or give alternatives since eggs are so high up on the allergen list for many people. Any substitute recommendations? Thanks.

Mariel Heiss February 23, 2018 at 11:49 am

Hi Tammy – thanks for your comment. I understand eggs can be an issue for many people!

I have a few suggestions –

If you tolerate flax (to be clear, Flax is illegal on SCD) – you could try substituting flax eggs

My favorite egg substitute is 1 tablespoon Gelatin (plain) mixed with 3 tablespoon of warm water (this replaces 1 egg, so you’d need to triple it for this recipe). Let the gelatin and water sit for a few minutes before you add it to the recipe (so it can firm up a bit).

Hope this helps!