Natto (Japanese Fermented Soybeans)

Making your own natto—Japan's famously slimy fermented beans with a subtle coffee aroma—allows for nearly endless customization.

Side angle view of natto being picked up with chopsticks

Serious Eats / Lorena Masso

Why This Recipe Works

  • Soaking the beans helps them fully and evenly hydrate, allowing for faster and more consistent cooking.
  • Adding the bacteria, B. subtilis, while the beans are hot encourages the microbes to reproduce and kickstarts the fermentation process. 
  • Using shallow containers for fermentation allows for better distribution of heat, more surface area exposed to the air, and a more even fermentation.

Natto is everywhere in Japan. Styrofoam packages of fermented soybeans line the refrigerated shelves of supermarkets and convenience stores. There’s natto made with large, small, or organic beans, and there’s hikiwari, or chopped up natto. Often, you’ll find natto with tare or other seasonings included in the package. Though natto is pretty simple to make, very few people do it. Like yogurt, most people are happy to grab a package of their favorite brand at the store.

As with many foods that are fermented and slightly funky, natto can be a challenge to the uninitiated. My enthusiasm for eating and making it has spooked even the most adventurous eaters among my friends. I get it: it's brown, its subtle coffee aroma is unexpected, and when you mix it with a pair of chopsticks the beans produce long, sticky, mucilaginous strands. It's a lot! But once you acquire a taste for it, there are few things that are as delicious. 

Overhead view of natto plated on rice

Serious Eats / Lorena Masso

If you want to try natto, it's widely available for purchase in Japanese specialty supermarkets and locations of H Mart. You may be wondering: if it's accessible here, too, why bother making my own? Many people, including Ann Yonetani of NYrture New York Natto, claim that freezing natto—as is common with the mass-market products—decreases many of its purported health benefits. My mother believes this, too, and it's what got her started with making natto at home.

The main reason why you should give making natto a try is that homemade natto is tastier and, well, funkier than the stuff you can buy in the package. Making your own natto also allows for nearly endless customization. For example, using black soybeans yields a milder and more toothsome natto than smaller brown soybeans. 

One note before you begin: Natto is distinct from other fermentations in that it is not as inhospitable to bad bacteria. Yonetani’s husband Zach Perlman, who co-runs the company, explains that while the low pH of foods like sauerkraut impede the growth of bad bacteria, natto is inherently high in pH, which some pathogens can tolerate. There were isolated incidents of reported food poisoning via homemade natto in the early 20th century, but using a commercial bacteria and keeping your equipment clean means that the risk of food poisoning in your kitchen is virtually nonexistent, provided you follow some basic steps.

Natto-Making Fundamentals

Natto consists of boiled soybeans that have been inoculated with a bacterium called B. subtilis (which is sold and known colloquially as nattokin, or natto bacteria), and then allowed to ferment. The sticky and gooey strands characteristic of natto are actually a bacterial biofilm that the probiotic cultures secrete.

Overhead view of natto bacteria

Serious Eats / Lorena Masso

The fundamentals of natto are very similar to that of yogurt, but instead of heating milk, you cook the beans to provide a hospitable environment for the bacteria starter. Once you add the starter, you put the beans somewhere warm so the bacteria can propagate and transform cooked soybeans into natto. Here are a few guidelines to follow to ensure success:

  1. Soaking the beans is essential. Aim for 12 hours if you can swing it. This helps them fully and evenly hydrate, allowing for faster and more even cooking. 
  2. The bacteria must be added while the beans are hot (as in, still fresh off the stove), as B. subtilis is heat-activated. Keeping the beans in a warm place then encourages the bacteria to reproduce and kickstart the fermentation process.
  3. All utensils and containers should be as sterile as possible (via boiling water) to reduce the chances of contamination by unwanted microorganisms.
  4. The containers for the fermentation must be relatively shallow. This allows for better distribution of heat, more surface area exposed to the air, and a more even fermentation. This particular fermentation requires oxygen (but only a small amount, which explains the tight lids called for in natto fermentation) and a deeper vessel brings with it the risk that the oxygen will not be evenly distributed. The beans are done after 20 to 24 hours; you should be able to see a light, white film coating the beans. If you see beans that don’t turn at all white, or don’t emit any scent at the end of 20 to 24 hours under a blanket, it’s likely you didn’t add enough starter, or that the setup was not warm enough.
  5. After the warm fermentation, you must chill the natto for 12 more hours before it is ready to eat. During this time, the flavor will continue to develop and the bacteria will continue to break down the proteins.

Choosing Soybeans for Natto

As stated above, the beauty of fermenting your own beans is that you can decide what kind to use. If you prefer a larger soybean, go with that. Black soybeans? Same story. All of the beans will ferment similarly, so long as they are thoroughly boiled. The black soybeans and the larger soybeans yield a milder natto which might be more palatable for beginners. The key is to keep an eye on them while they cook, as different bean varieties will have different cooking times. 

Some sources for quality beans include Shiloh black soy beans, Hunza organic soybeans, and Signature Soy Non-GMO Soybeans for Natto (these soybeans are small, as is classic of packaged natto).

Required Equipment

You’ll need some sturdy, non-reactive, flat, rectangular vessels (like glass baking dishes) and somewhere warm to incubate your beans. Some cooks put the beans in an oven with its light switched on (also a common trick for incubating yogurt), but Michiko swears by an electric mat that she covers with a blanket. Experiment with what works. The key is to keep the natto at somewhere around 100°F (38°C) for 24 hours. 

What to Look For When Making Natto

A visual cue for successful fermentation is the presence of white strands coating the beans. However, if you incubate the inoculated beans at temperatures warmer than 100°F,  it’s possible that the strands won't form by the end of the 24 hour cycle. If that's the case, you have to open the container and take a whiff. If it reminds you of some very funky cheese, you’re in the clear. Move the containers to the refrigerator and let them ferment for an additional 12 hours. If not, you'll have to throw them away and start over. (You could eat them, but they'll just be bland, cooked soybeans that have been sitting out longer than is advisable.)

Close up view of natto

Serious Eats / Lorena Masso

How to Enjoy Natto

The classic way to serve natto is mixed with tare and served over rice, which is why every package of natto sold in Japan is accompanied by its own mini packets of tare and karashi mustard. Tare is usually salty from soy and also a little sweet, so a 1:1 mix of mirin and soy is a good alternative if you can’t find tare. Other tares add things like a tangy umeboshi flavor, so you can also chop up some umeboshi and add it to yours. However, natto is delicious in so many other applications. If you have some mentsuyu (a Japanese soup base) knocking around in your fridge, this is a good place to use it as well. Other ideas include:

  • Salad: Mix the natto with diced tomatoes and cucumbers. Add salt and pieces of shiso leaf if you have it. This is so refreshing and can temper the funkiness for those new to natto. 
  • Over soba: This is a classic presentation that showcases the Japanese love for things that are neba-neba (stretchy and gooey). Pour some natto over a bowl of cooked, rinsed soba, some slices of blanched okra, and some grated yamaimo if you have it. Shower your bowl with shiso and a splash of mentsuyu. 
  • With kimchi: My mother's favorite, this double punch of fermentation pairs the salty-sour tang of kimchi with natto’s earthy alkalinity. 
  • Over pasta: Yes, this is a Japanese classic. Toss hot spaghetti with some natto, olive oil (or sesame oil for a different flavor profile), soy sauce, and a little bit of pasta water. Serve it with nori and shiso.

Recipe Details

Natto (Japanese Fermented Soybeans)

Prep 12 hrs
Cook 3 hrs
Fermentation Time 36 hrs
Total 51 hrs
Makes 4 cups

Making your own natto—Japan's famously slimy fermented beans with a subtle coffee aroma—allows for nearly endless customization.

Ingredients

  • 2 cups dried soybeans (10 1/2 ounces; 300g)
  • Half of 1/8 teaspoon natto starter spores, such as Nattomoto

Directions

  1. Place dry beans into a large pot. Cover the beans with water and soak for at least 8 and up to 12 hours.

    Soybeans in a bowl

    Serious Eats / Lorena Masso

  2. If Cooking On the Stovetop: Rinse soaked beans thoroughly, then return to pot. Cover beans with at least 1 inch of fresh water and bring to a boil over high heat. Reduce heat to maintain a steady simmer and cook until beans are completely tender but still whole, about 4 hours (see notes). Meanwhile, pour boiling water into a large, heatproof mixing bowl, making sure boiling water touches most of the inner surface to sanitize it, then drain. Drain beans and transfer to the large mixing bowl. Discard the cooking liquid.

    Soybeans boiling in pot

    Serious Eats / Lorena Masso

  3. If Using a Pressure Cooker: Rinse soaked beans thoroughly in 3 changes of fresh water. Cover beans with at least 1 inch of fresh water. Seal the pressure cooker lid. Bring to high pressure and cook for 10 minutes. Allow pressure to release naturally. The beans should be completely tender but still whole (see notes). Meanwhile, pour boiling water into a large, heatproof mixing bowl, making sure boiling water touches most of the inner surface to sanitize it, then drain. Drain beans and transfer to the large mixing bowl. Discard the cooking liquid.

    Cooked beans draining

    Serious Eats / Lorena Masso

  4. Meanwhile, boil a stainless steel teaspoon, a stainless steel soup spoon, and a small metal bowl in water for 5 minutes; transfer sterilized utensils to a clean work surface. Pour boiling water into the containers you will use to ferment the soybeans, then drain. In the sterilized small bowl and using the sterilized teaspoon, mix the natto starter spores with 1 tablespoon of water and immediately add to the hot soybeans (the soybeans must be hot, as this bacteria is activated by the heat). Using the sterilized soup spoon, mix soybeans very thoroughly to ensure the starter is evenly distributed throughout.

    Two image collage of natto starter and adding to soybeans

    Serious Eats / Lorena Masso

  5. Divide beans into the sanitized wide airtight containers (each container of beans should have a layer of beans no more than 2cm deep). Cover with cheesecloth and seal with the lid.

    Two image collage of cooked soybeans added to containers and covered with cheesecloth

    Serious Eats / Lorena Masso

  6. Set the containers in a warm place; you can use a yogurt maker, a proofing drawer, or a turned-off oven with the oven light on; the important thing is that your beans are in an environment of about 100ºF (38ºC). Let stand, rotating the container positions after about 12 hours and checking every hour starting around the 20th hour, until the beans are covered all over in a thin white film and smell cheesy and nutty, 20 to 24 hours; see notes for more on what to do if your soybeans don't look and smell like this.

    Two image collage of soybeans in an oven and finished fermented soybeans

    Serious Eats / Lorena Masso

  7. Transfer containers to the fridge and allow beans to continue to ferment for 12 hours. The natto is now ready to eat.

    Overhead view of natto plated on rice

    Serious Eats / Lorena Masso

Special Equipment

Wide, airtight, nonreactive containers (such as glass baking dishes)

Notes

If you prefer beans with a little more chew, this recipe will work if you boil them a little less. This is your natto, make it as you like!

Natto can ferment unevenly, especially if the starter wasn't mixed in thoroughly, or the fermentation temperature was uneven. If you still see white film on most but not all of the natto, you can give it a good stir, then continue with the recipe by transferring natto to the fridge to finish.

If your beans fail to turn white, and don’t emit any scent at the end of 20-24 hours, it’s likely you did not add enough starter, or that the setup was not warm enough. I recommend starting over from scratch.

If you over-ferment the beans, they will become stiff and hard to mix (albeit, still edible).

Make-Ahead and Storage

Natto will keep for 2-3 weeks in the fridge, but will get more pungent with time. I once rediscovered a jar of Michiko’s natto that had been sitting in the fridge for over a month and it almost knocked me off of my feet.