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Healthy Home Economist / Archives / Recipes / Legume Recipes / White Natto (soy-free, low starch, gut friendly)

White Natto (soy-free, low starch, gut friendly)

by Sarah Pope / Jun 24, 2026 / Affiliate Links ✔

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Table of Contents[Hide][Show]
  • Why You Need Natto in the Diet
  • White Natto+−
    • Ingredients
    • Instructions

How to make natto from low-starch navy beans that are permitted on gut healing protocols that limit almost all other legumes to facilitate healing of the microbiome.

white, starch-free natto in glass jar with spoon

Natto is the best fermented food to obtain soil-based probiotics (SBOs) in the diet.

That said, there are some issues with traditional natto made with soybeans.

First, soybeans are the food highest in plant estrogens. While this isn’t a problem for those with balanced hormones, for those with hypothyroid or other hormonal issues, soya is best avoided even in healthy, fermented form (culturing does NOT lower the goitrogens).

This is the main reason I developed my soy-free natto recipe posted a couple of years ago. It is made out of mung beans, which most closely resemble tender soybeans in size and texture.

Second, soybeans are high in starch and disallowed on gut healing protocols like GAPS. So even if a person has healthy balanced hormones, natto is not a legal food when healing the gut and limiting starch.

Soy-free mung bean natto doesn’t work for GAPS either as this legume, like soybeans, is fairly high in starch.

So, I developed a different form of natto that everyone can eat, no matter if on GAPS or struggling with hormone balance issues.

This “white natto” as I call it, is made out of navy beans, one of the very few legumes that are low starch and permitted on gut healing protocols like GAPS.

If you think that you don’t need natto because you already consume a variety of fermented foods and beverages, I would suggest reconsidering.

Why You Need Natto in the Diet

Natto is very unique in that it contains Bacillus subtlis, a soil based probiotic that is incredibly helpful to health. No other fermented food contains this strain in the large quantity that natto does.

According to microbiome researcher, entrepreneur, and BiotiQuest Founder Martha Carlin, B. subtlis used to be known by the common name “Hay bacillus”. (1)

If you think about it, we were out in the fields and the grasses, and we were breathing it [B. subtlis] in. It is a really interesting organism…it makes a frequency that sort of knocks out pathogenic organisms. And, it’s also self-sacrificing, so if there’s not enough food for it [in the gut], it will sacrifice part of the colony to feed itself [unlike other microbes that start to eat the intestinal mucin if there isn’t enough food for them]. So, it’s a really interesting, what I would call “team player.” (2)

Natto is also extremely high in Vitamin K2 (~150 mcg/tablespoon) that is crucial for cardiovascular health as well as strong teeth and bones.

It would be very beneficial to find a way to incorporate natto into the home menu!

white natto in glass jar with spoon
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White Natto

How to make natto from low starch navy beans that are permitted on the GAPs diet or other protocols that limit carbs to facilitate gut healing.

Course Condiment
Cuisine Japanese
Keyword gaps, healthy, low carb, low starch, probiotic, soy-free
Prep Time 15 minutes
Cook Time 20 minutes
Soaking and Fermentation 1 day 8 hours
Total Time 1 day 8 hours 35 minutes
Servings 48
Calories 23 kcal
Author Sarah Pope

Ingredients

  • 1 cup dried navy beans unsprouted and organic
  • filtered water
  • 1 packet natto spores OR 1/4 cup previous batch

Instructions

  1. Rinse navy beans and place them in a large glass bowl. Cover with enough filtered water to allow the beans to roughly double in size as they expand. Leave on the counter for 8 hours or overnight.

  2. Drain the soaking water and place beans in a large pot. Cover with fresh filtered water.

  3. Bring the beans to a boil, turn down the temperature to a simmer, affix the lid and cook the beans for 45 minutes until soft but not mushy.

  4. Drain the beans and place in a large VitaClay slow cooker or crockpot. The beans should be no more than 1" in depth. Discard any beans that may accidentally spill during the transfer from the pot to the cooker.

  5. Let the beans cool for 10 minutes.

  6. While the beans are cooling slightly in the Vitaclay or slow cooker, dissolve a packet of natto starter in 3 Tbsp of warm filtered water. Alternatively, use 1/4 cup of your previous white natto batch as the starter.

  7. Place the lid on the VitaClay and select the "yogurt" setting.

    If using a different type of slow cooker, use the setting that will keep the beans between 100-110 °F/ 38-43 °C which is the temperature range necessary to ferment the beans into natto.

  8. After 24 hours, turn off the Vitaclay, remove the lid, and cool the natto to room temperature for 1 hour. A whitish film and an ammonia-like aroma means they are done. The beans will also have a stringy and slimy appearance (see photo above).

  9. Place the cooled natto in a glass container with a tight-fitting lid and refrigerate.

  10. Natto will be ready to eat once refrigerated overnight. It will last for months, and the flavor will age and strengthen with time.

  11. Navy beans are low starch and legal on the GAPs diet. They are also soy-free, so 1-3 tablespoons per day is a safe and inexpensive soil-based probiotic source as well as an excellent Vitamin K2 food source.

Nutrition Facts
White Natto
Amount Per Serving (1 Tbsp)
Calories 23 Calories from Fat 9
% Daily Value*
Fat 1g2%
Saturated Fat 0.1g1%
Polyunsaturated Fat 0.5g
Monounsaturated Fat 0.4g
Potassium 33mg1%
Carbohydrates 2.5g1%
Fiber 2g8%
Protein 1g2%
Calcium 4.5mg0%
Iron 0.2mg1%
* Percent Daily Values are based on a 2000 calorie diet.

References

(1, 2) The Microbiome Revolution with Martha Carlin

low starch natto on glass jar
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Category: Fermented Side Recipes, GAPS Recipes, Gluten Free Recipes, Legume Recipes, Low Carb Recipes, Paleo Recipes, Vegetarian Recipes
Sarah Pope

Sarah Pope MGA has been a Health and Nutrition Educator since 2002. She is a summa cum laude graduate in Economics from Furman University and holds a Master’s degree from the University of Pennsylvania.

She is the author of three books: Amazon #1 bestseller Get Your Fats Straight, Traditional Remedies for Modern Families, and Living Green in an Artificial World.

Her four eBooks Good Diet…Bad Diet, Real Food Fermentation, Ketonomics, and Ancestrally Inspired Dairy-Free Recipes are available for complimentary download via Healthy Home Plus.

Her mission is dedicated to helping families effectively incorporate the principles of ancestral diets within the modern household. She is a sought after lecturer around the world for conferences, summits, and podcasts.

Sarah was awarded Activist of the Year in 2010 at the International Wise Traditions Conference, subsequently serving on the Board of Directors of the nutrition nonprofit the Weston A. Price Foundation for seven years.

Her work has been covered by numerous independent and major media including USA Today, ABC, and NBC among many others.

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