GAPS Diet Flours for Baking

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I’m sharing the best GAPS diet flours for baking in this handy guide.

GAPS flours for baking

GAPS diet flours for baking

Choosing the best GAPS diet flours for baking doesn’t have to be difficult. In fact, this diet lays out a few of the simplest flours for you and your family to bake with that fit best with the GAPS diet. 

There are a lot of flour varieties that can be used on the GAPS diet. There are some that you should definitely avoid and then there are specific ways that you can incorporate the GAPS approved flours into your diet. 

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The guide to baking on the GAPS diet

I recommend the book The Complete Cooking Technique for the GAPS diet by Monica Corrado (the official GAPS chef). This book is wonderful and does an excellent job laying out the flours that your body will do the best with.

In the book, Corrado talks of four approved flours: 

  1. Homemade almond flour (or other nut or seed flour)
  2. Homemade coconut flour
  3. Coconut butter/coconut manna (this is simply coconut pureed)
  4. White Navy beans can also be used, but it is a long, laborious option. It is a substitute that can be used if nuts and coconut are not an option, and someone really wants baked goods.

Corrado also mentions one alternative, but with a strong warning that I always like to keep in mind. 

Nut flours from the store can be used in a pinch, but I try really hard not to use store bought almond flour or almond flour that you do not process thoroughly enough. This is because almonds are seeds and hold a lot of anti-nutrients on them. This can make your digestive system have to work extremely hard – not our goal on GAPS!

Also, store bought nut flours often sit around on the shelves for a long time and go rancid before you buy them.

How to make GAPS diet flours for baking

Luckily, making your own GAPS diet flours for baking is a fairly simple process. In fact, I usually plan out my baking to just add it into one of the steps. 

Take your nuts or seeds, soak, ferment, or sprout them, dry them out, and then grind them for a hearty flour that is also kind to your digestive system. I’ll go into more detail on the exact step by step process later in this post. 

Or you can make your own coconut flour. I’ll also explain coconut flour below. Coconut manna is also a great option for flourless baked goods. I’ll be sharing a flourless cupcake recipe that uses coconut manna in a new blog post very soon. 

It can take some time, but it is a really easy process to make flour for all of your GAPS approved baked goods. 

To see how simple it really is, keep reading to learn how to make homemade flour…

Things to note when making GAPS diet flours

There are so many diet flours out there, it can be overwhelming to choose which is best for your homemade baked goods. That is one reason that I love the GAPS diet – it keeps the recipes simple and wholesome. This includes flours for your birthday cake!

Here are a few things to keep in mind for when you are making your own GAPS diet flours for baking…

  • When making your own flours, the fresher the better. If possible, plan ahead of your baking so that you can soak your almonds long enough or have enough time to dry out the blended coconut solids.
  • With shredded coconut, be careful to buy as natural as possible. Oftentimes, shredded coconut will come with added sugar and chemicals that can be harmful to your body while on the GAPS diet. I personally only buy my Shredded coconut from Azure Standard, so that way I am sure the ingredients are fresh and wholesome. 
  • Pay attention to how your body responds to the flour. 
  • Avoid store bought nut and especially coconut flours! They are very harmful to a digestive system that is working hard to heal. 
  • If you have extra, be sure to store in an airtight container in the freezer. Any exposure to air will ensure that your homemade diet flour will go rancid very quickly. 
  • A high quality food processor will help you get the smoothest flours for your baked goods. Personally, I love to use this one for creating fine flours.
  • When grinding the flour, make sure to stop soon enough – if you blend too long you’ll end up with nut butter.

Ready to learn how to make both nut flour and coconut flour? Keep reading to see the exact steps and how easy these GAPS diet flours really are…

How to make nut flour

To make almond flour takes a little bit of planning ahead (since soaking can take some time), but aside from that it is a fairly simple process. 



  1. Soak/sprout/ferment nuts or seeds for at least 12 hours (longer is even better)
  2. Dry them out with a dehydrator or in the oven on the lowest temperature possible until dry
  3. Grind them into flour using a food processor or high powered blender
  4. Or, another method is to grind the nuts or seeds first, and then soak or ferment the flour for 12 – 24 hours

How to make coconut flour

In my experience, coconut flour makes some of the sweetest, most delicious baked goods around! The fact that it helps your gut heal is just icing on the cake. 



  1. Add shredded coconut to the blender with equal parts warm water
  2. Blend
  3. Strain the solids from the liquid and save the coconut milk for other uses
  4. Spread out the solids and let them dry in a dehydrator or in the oven on the lowest possible temperature for one hour

Choosing nuts and seeds

It is important to discuss the value in quality nuts and seeds for your flours. Personally I love to order mine from Azure Standard, where you can get the highest quality for your flours. 


To soak almonds, all you need is to fully submerge your whole nuts or seeds in water for 12 – 24 hours. This will make the nuts easier to digest, unlock the nutrients, and deactivate the anti-nutrients. 

Or, like I said above, you can alternatively grind the nuts or seeds first, and then soak or ferment the flour. 

If soaking is too big of a hassle, I recommend making coconut flour instead. As mentioned in the recipe above, all of the hard work is at the beginning where you blend and strain the shredded coconut first. Then you dry the coconut flour before you start baking.    


To ferment nuts or seeds, the process is the same as soaking, except that you add some whey from dripping homemade yogurt or kefir to the soaking water. You can also soak nut or seed flour in water and whey. 

Coconut flour vs almond flour         

When it comes to using coconut flour or almond flour in your baked goods, one thing is for sure – store bought is not the way to go. 

Store bought almond flour often is a bag of rancid almonds, so your body will not receive all of the proper benefits from the food. 

Store bought coconut flour is very high in fiber and can be very irritating to a healing gut. In her book, Corrado describes it as like rubbing sandpaper on a wound. Ouch!

Homemade almond (or other nut or seed) flour and coconut flour can be great options on the GAPS diet. Some people tolerate one better than the other. I recommend listening to your body and going with the one that your body likes the best.

GAPS diet cassava flour

Cassava flour is a gluten-free option that is, unfortunately, not approved on the GAPS diet. This is because starches feed pathogens, and for that reason, are avoided on GAPS. Later, when transitioning off of GAPS, cassava flour is one of the first starches that can be introduced. 

GAPS diet bread recipe

The flours I’m about to share are perfect for making GAPS bread. Dr. Natasha has a basic bread recipe in her books, and I’m also going to share my favorite GAPS bread recipe soon in an upcoming blog post.

Keep reading to learn how to properly store any leftover GAPS diet flours for the rest of your baking…

How long do GAPS diet flours last?

All GAPS diet flours are best stored in the freezer, where they will last several months. I like to keep mine in glass jars or glass storage containers. 

More GAPS recipe

GAPS Diet Pumpkin Muffins

Blended Carrot Soup Recipe

Fermented Beets Recipe

Have you ever made your own GAPS baking flour?

If you did, what did you make? What methods did you use? Comment below and let us know!

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Looking for a GAPS Intro meal plan?

GAPS to Go is a 30 day meal plan for the GAPS introduction diet that tells you what to eat each day, with complete cooking instructions, and guidance on when to move to each intro diet stage.

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GAPS to Go Meal Plan for the GAPS Diet

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The information in this blog post is my personal experience and opinion. It is for general information purposes only, that may not apply to you as an individual, and is not a substitute for your own physician’s medical care or advice. Always seek advice from your physician or another qualified health provider with any questions you may have regarding nutrition, medical conditions, and advice. Never disregard medical advice or delay seeking medical care because of something you have read on this blog.


2 thoughts on “GAPS Diet Flours for Baking”

  1. Looking for some clarification on soaking flours. You mention, “Or, another method is to grind the nuts or seeds first, and then soak or ferment the flour for 12 – 24 hours.” Do you happen to have specific instructions for this method somewhere? Thank you!

  2. Hi Marisa! Thank you for all the information you provide. I would not have been able to complete 67 days (and counting) of the GAPS without your help and it has so drastically saved my life. I loved the coconut manna cupcake recipe and would like to bake a batch of flourless Christmas cookies with the same type of ingredients as the cupcakes. Can I take a non-GAPS christmas cookie recipe and substitute the amount of all-purpose flour with coconut manna? What is the substitution conversion for coconut manna when used instead of flour? So far I’ve been scraping the web for GAPS Christmas cookies and have not been able to find anything that is trustworthy. Thanks in advance for your help!


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