How to Make Natto + Health Benefits

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If you want to learn how to make natto, you are in for some surprises.  This is because this food is very easy to make and has some exceptional health benefits.  

Making this it at home can save you a lot of money too.  

While some people with thyroid disorders should avoid soy, homemade natto is fermented and many of the compounds that interfere with thyroid function are eliminated by fermenting the beans. 

While natto is easy to make and also inexpensive,  it is going to take a little planning. The fermentation process will also take a few day’s time, so make sure to plan ahead.

Don’t worry, you don’t have to hover over it as it ferments, so you are not tied to the kitchen all day!

Bowl of brown natto beans in a clear glass bowl with three glass jars of natto beans behind it against a orange wall with the words "health benefits of natto" in green against a white background How to Make Natto + Health Benefits | Thyroid Nutrition Educators

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What Do You Need to Make Natto?

To get ready for fermenting soybeans, you will want to make sure you have some equipment staples and food items on hand for this.  

Gather up the following:

The process is simple.  First sterilize all your containers, lids, and spoons. You can do this by washing everything with soap and rinsing it with water.  

Many of these recipes call for cheesecloth, but I’ve made it without cheesecloth and it turns out just fine.

Natto How-To Video

Here is a quick video to show you the basics of natto making:

Sterilize Your Equipment

For the best quality product, you want to make sure everything is very clean.  So you first should place the spoons you will use in a small pot with boiling water for 5 minutes.  Boiled water is used to clean your utensils. 

To sterilize your glass containers and lids, place them in the oven at 200 degrees Fahrenheit (93 degrees Celsius)  for 10 minutes. 

I recently discovered that you can also just place them in a microwave for 60 seconds and achieve sterilized containers too. Just make sure to wash them first. 

Soaking the Beans

You need to soak your beans to make the nutrients more available to you and to make the ferment occur.  

The soaking process also reduces anti-nutrient compounds and lectins too. 

Grab a large saucepan and add the organic soybeans.  By the way, organic beans are recommended for optimal probiotic formation. 

Cover the beans with 3 parts water for every 1 part beans.  In other words, make sure they are covered in a lot of water so the beans have the ability to hydrate and expand. 

Go ahead and soak these beans for around 9 to 12 hours.  You can soak them for longer and it won’t hurt either, just try to cook them on the second day. 

Cooking the Beans

After you have soaked the beans, you will want to rinse them and then fill it with another 3 parts of water for every 1 part beans.  The pan is going to be very full at this point.  Bring the beans to a boil, then reduce your heat to a low simmer.  

A foam will form at the surface and this is normal.  Scrape this foam layer off and discard it. Boil the beans between 3 to 4 hours until they are tender and soft, but not mushy.  Test them along the way by checking their texture.  

Once the beans are soft, drain off all the water using a clean colander

Fermenting the Beans

Bacillus subtilis is the type of probiotic that ferments natto. 

For the fermentation process, you will need only 3 things: bacillus natto bacteria, sterilized water, and organic soybeans.

Your natto bacteria will come with a special spoon and you are going to want to scoop one tiny spoon of this culture into 2 tablespoons of sterilized but cooled water.  Set this aside for now. 

Place your cooked soybeans that are still warm, but slightly cooled, into the pressure cooker or Instant Pot.  The beans should only be about an inch thick.  Set any remaining beans in the refrigerator so that you can ferment them on the second day. 

Then, go ahead and sprinkle the culture onto the beans and mix it in thoroughly. *Note: some people make natto without a starter and will add a small amount of premade natto into their soybeans. 

I haven’t tried this method yet, but some people say that this version isn’t as potent as using a starter culture.  

Time and Temperature for Fermenting

Cover the bean mixture with the pressure cooker lid. 

You will want your Instant pot set on the lowest setting to achieve about 100 degrees Fahrenheit or 37 degrees Celsius for about a day, about 22-24 hours. 

My oven doesn’t keep that temperature because even the warm setting is too hot. So I decided to use my Instant pot yogurt setting. The best pressure cooker setting to keep on warm is the normal yogurt setting, but just make sure you don’t get the heat too high or the fermenting process will halt. 

During this stage, some people swear that the scent of the beans is like a strong ammonia smell. 

I didn’t find this to be true for me. If so, crack a window, and it won’t be bothersome at all. Even my kids didn’t even notice the smell!

The beans smelled warm and pleasant, but we all have our own perceptions of fermented foods and their aroma!

Aging the Beans

After you remove the beans from the pressure cooker, you will want to age them for a day or two in the refrigerator.  Keep the lids on. 

You can keep the beans here for up to five days, but go ahead and eat them whenever you wish. 

If you don’t use the beans by the 5th day, make sure to freeze any extras.  The finished product will be good for a few months and you can take it out as needed. 

Natto Taste

The flavor of Japanese natto, while unique, is quite pleasant to me.  Some people don’t love the texture, but I find that the texture pairs well with soup and rice. 

It adds a nice umami flavor to dishes, so mixing it into dishes is a good way to disguise the sticky, sometimes slimy,  texture. 

Another way to eat it is to add a tablespoon of natto to a sushi roll.  Top with a little coconut amino and some pickled ginger.  Using natto doesn’t have to be limited to Japanese cuisine.  Get creative and combine the flavor fusion with other food, such as tacos.  

Brown natto beans in a clear bowl with a silver spoon and green leaf garnish and words saying "How to Make Natto"|How to Make Natto| Thyroid Nutrition Educators

Natto Recipes

You have natto, now what?

Here are some recipe resources we have compiled so that you can eat your natto in abundance. 

There really is no wrong way to use natto.  Be creative. 

Buy Natto Starter

You can buy natto spores online or perhaps in specialty grocery markets that sell Japanese natto bean supplies.

The kind I used is called Nattomoto, but with the recent surge in popularity, it is not available for sale at this time.

Natto Health Benefits

We really want you to be familiar with this healing food. 

Natto is difficult to find, so making natto is really worth your time because the ingredients are simple: organic soybeans and natto spores. 

From boosting immunity to helping your bone health, here are some of the main known health benefits of natto:

Natto Nutrition

Natto is very nutritious and contains some compounds that are only found in natto too, such as nattokinase.

Made from soybeans, natto is also rich in protein.

Vitamin K2:

Natto has more vitamin K2 than any food on the planet by far with over 500 mcg per serving according to

A deficiency of vitamin K2 is rampant and is different from a deficiency of vitamin K1.  Most tissues in the body use vitamin K2 to activate proteins in the body. Intake of vitamin K2 is highly related to heart health, strong bones, and may help with thyroid health.  

Vitamin K2 works synergistically with vitamin D and vitamin A to keep hormone balance. This critical nutrient may help balance out estrogen by balancing calcium in the body. 


Probiotics support healthy thyroid function by dampening down the autoimmune disease and restoring immune tolerance. Natto is a very rich source of probiotics, according to Healthline, containing up to 1 billion CFU’s per gram.   

Natto contains a unique strain of probiotics called bacillus and it is not found in other foods.

While natto is cultured in the bacillus strain of bacteria, the development of a broad spectrum of probiotics occurs during the fermentation process, such as lactobacillus probiotics. 

We wrote an extensive post about probiotics for leaky gut, which describe how probiotics may help our whole body, including the thyroid. 

Unlike most probiotic foods, natto is a salt-free fermented food, which makes it an ideal menu item for people needing to limit sodium.  

Immune Boosting

Natto probiotic is called bacillus, which is a soil-based probiotic. These are stable at room temperature for much longer than lactobacillus strains, which means they don’t lose their potency as easily.

Probiotic foods like natto may help immune function. Innate immune cells known as macrophages are activated when given the bacteria culture found in natto.

Bacillus probiotic also activated immune cells in a group of elderly people during the cold season and tended to reduce the duration and severity of colds. However, more research is needed as the cold incidence differences from the placebo didn’t reach significance.


Natto also contains an enzyme called nattokinase, which is another unique substance found only in this food.

Nattokinase has been used in many cultures for medicine because it has strong blood clot inhibition effects in the body. How does nattokinase work?  It breaks down fibrin and plasmin activator inhibitor (PAI-1) while increasing the plasminogen activator.

With such strong effects, one might wonder about safety.  The good news is that it is safe when eaten in natto form.

Clinical studies even find that nattokinase may help reduce heart disease and Alzheimer’s disease risk, although more work is needed.

We recommend eating natto instead of supplementing nattokinase at this time.

Other Vitamins and Minerals

A cup of natto contains 1275 mg of potassium, which meets about 30% of your daily needs.

It is also is rich in magnesium, vitamin B6

For more information about the mineral content of natto, read more at Eat This Much.

Natto Allergy Considerations

If you are allergic to soybean, natto isn’t the right choice for you.  You can also make natto from other beans like garbanzo beans and black beans, according to Cultures for Health

However, many people who have soy intolerance can eat natto because the fermentation process breaks down compounds that are hard to digest.


Making natto is very rewarding because of the high amounts of nutrients and probiotics you will reap from it.  Some individuals cannot tolerate soy but they may be able to consume fermented soybeans like natto. As always nutrition should be individualized to that person’s specific needs.

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