Natto (Japanese Fermented Soybeans) Recipe

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. 

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.

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.)

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.