Making natto at home requires just three things: soybeans, a bacterial starter, and a warm spot to ferment for about 18 to 24 hours. The process itself is simple, but the details matter. Getting the beans soft enough, keeping the temperature steady, and knowing when to stop fermentation are the differences between sticky, nutty natto and a batch that smells like cleaning products.
Choosing the Right Soybeans
Smaller soybeans make better natto. Natto-type soybeans are typically less than 5.8 mm in diameter with a thin seed coat and a clear hilum (the small spot where the bean attached to the pod). The reason is straightforward: the fermenting bacteria need to penetrate all the way to the center of each bean, and smaller beans make that easier. You can find small Japanese-style natto soybeans online or at Asian grocery stores, often labeled “natto soybeans” or “small soybeans.”
Standard large soybeans from a health food store will work in a pinch, but expect a chunkier texture and less even fermentation. Avoid split soybeans or old stock that’s been sitting on a shelf for years, as the beans won’t hydrate evenly.
Soaking the Beans
Start with about 2 cups (roughly 400 grams) of dry soybeans for your first batch. Rinse them well, then cover with plenty of water. The beans will roughly double in size, so use at least three times as much water as beans by volume.
At room temperature, soybeans need around 12 hours of soaking. In warmer weather (above 25°C/77°F), 8 to 10 hours can be enough. In a cold kitchen during winter, plan on the full 12 or even up to 16 hours. The target is beans that have absorbed enough water to swell fully, with smooth, rounded surfaces and no wrinkled spots. If you cut a bean in half, the interior should be uniformly colored with no dry, opaque core.
Water content matters for what comes next. Research on steamed soybeans shows that beans need to reach at least 80% water content before cooking to avoid producing hard natto. Thorough soaking is the easiest way to get there.
Cooking Until Very Soft
Drain and rinse your soaked beans, then cook them until they’re extremely soft. You should be able to crush a bean easily between your thumb and pinky finger with almost no resistance. If you have to squeeze hard, they need more time.
A pressure cooker is the most practical method. Cook at high pressure (around 121°C/250°F) for 45 minutes to an hour. Without a pressure cooker, you can steam the beans for 4 to 6 hours or boil them for 3 to 4 hours, though a pressure cooker produces better texture. Research on natto production found that steaming at 121°C for a minimum of 15 minutes prevents hard natto, but that’s industrial steaming at precise pressure. At home, err on the side of longer cooking.
Steaming is generally preferred over boiling because it keeps more nutrients in the beans and produces a firmer, less waterlogged texture. But boiling works fine, especially if you don’t own a steamer setup large enough for a full batch. The critical thing is softness, not the method you use to get there.
Inoculating With Starter
You have two options for introducing the bacteria that transform cooked soybeans into natto.
- Natto spore powder (natto-moto): This is the most reliable method. You can order it online from Japanese suppliers. A tiny amount goes a very long way. Follow the specific instructions on your packet, as concentrations vary between brands. Typically, you’ll dissolve a small measure of powder in a few teaspoons of warm (not hot) sterilized water and mix it into the beans.
- Store-bought natto: Mix roughly half a tablespoon of commercial natto into your cooked beans. The existing bacteria will colonize the fresh soybeans. This is convenient and cheap, but the fermentation can be less predictable since commercial natto contains aging bacteria alongside active ones.
Timing matters here. Add the starter while the beans are still warm (around 40 to 45°C/104 to 113°F), not hot enough to kill the bacteria and not cool enough for other microbes to get a foothold. Mix thoroughly so every bean gets contact with the starter. Use a sterilized spoon rather than your hands, since you don’t want to introduce competing bacteria.
Setting Up the Fermentation Container
Spread the inoculated beans in a shallow layer, no more than 2 to 3 centimeters (about an inch) deep. The bacteria are aerobic, meaning they need oxygen to thrive. Deep piles of beans suffocate the organisms at the bottom and produce uneven results.
Traditional natto is fermented in rice straw bundles, but at home you can use shallow glass containers, stainless steel trays, or even Styrofoam takeout trays. Cover the beans with a layer of perforated plastic wrap, cheesecloth, or a clean kitchen towel. You want air circulation while preventing the surface from drying out.
Fermentation: Temperature and Timing
This is the step that makes or breaks your natto. The target temperature is 40 to 42°C (104 to 108°F) with humidity around 85 to 90%. Maintaining this environment for 18 to 24 hours produces well-fermented natto with good stickiness and a mild, nutty aroma.
There are several ways to hold this temperature at home:
- Oven with the light on: Many oven lights generate enough heat to keep the interior around 40°C. Test yours with a thermometer first.
- Instant Pot or yogurt maker: The yogurt setting on many Instant Pots holds a temperature close to the right range. Some run a bit cool (around 37°C), which still works but may need a few extra hours.
- Cooler with warm water bottles: Place your container in a small insulated cooler alongside a couple of jars filled with hot water. You’ll need to swap the water every 6 to 8 hours to maintain temperature.
- Seedling heat mat: A reptile or gardening heat mat with a thermostat controller gives you the most precise control.
Check the temperature periodically. Below 35°C, fermentation slows dramatically and competing bacteria can take over. Above 50°C, you risk killing the natto bacteria entirely.
After 18 to 20 hours, check on the beans. Well-fermented natto will have a white, slightly filmy coating on the surface and will produce thin, sticky strings when you pull the beans apart. A mild, earthy smell is normal. If the beans look good at 20 hours, fermentation is done.
Why Ammonia Happens and How to Avoid It
A faint ammonia note is normal in fresh natto, but a strong, eye-watering ammonia smell means something went wrong. This typically results from secondary fermentation, where the bacteria start breaking down amino acids (especially glutamate) and urea in the soybeans, releasing ammonia as a byproduct. Research has identified two main chemical pathways responsible: the breakdown of glutamate by specific enzymes and the degradation of urea.
The most common causes at home are fermenting too long (past 24 hours), fermenting at too high a temperature, or leaving the natto at room temperature after fermentation finishes. The fix is simple: don’t let it go past 24 hours on your first batches, and move it to the refrigerator as soon as fermentation is complete. Refrigeration halts the secondary fermentation that produces ammonia.
Aging in the Refrigerator
Fresh natto straight from fermentation is edible but has a relatively sharp, one-dimensional flavor. Transfer your container to the refrigerator and let it rest for at least 24 hours before eating. Many natto makers prefer 2 to 3 days of cold aging, which mellows the flavor and improves the sticky, stringy texture.
Homemade natto keeps well in the refrigerator for 7 to 14 days when stored in a sealed container. Below 4°C, the enzymatic activity slows significantly but doesn’t stop entirely, so flavor will continue to shift gradually. After about two weeks, you may notice the stickiness declining and off-flavors developing. For longer storage, natto freezes well for up to 3 months. Thaw it in the refrigerator overnight before eating.
What Makes Natto Worth the Effort
Beyond the distinctive flavor and texture, natto is one of the richest food sources of vitamin K2 in the form called MK-7. Regular natto contains roughly 775 micrograms of MK-7 per 100 grams, which is many times the amount found in other fermented foods or cheeses. MK-7 plays a role in calcium metabolism, helping direct calcium toward bones rather than soft tissues. A single serving of natto (about 40 to 50 grams, one typical small package) delivers a substantial dose.
Natto also contains a protein-dissolving enzyme produced during fermentation that has been studied for its effects on blood clot breakdown. Combined with the probiotic bacteria, the complete protein of soybeans, and high fiber content, natto is nutritionally dense in ways that plain soybeans or tofu are not.
Quick-Reference Batch Summary
- Dry soybeans: 2 cups (about 400g), preferably small-seeded varieties
- Soaking: 12 hours at room temperature in triple the volume of water
- Cooking: Pressure cook 45 to 60 minutes, or steam 4 to 6 hours, until very soft
- Starter: Natto spore powder per package directions, or half a tablespoon of store-bought natto
- Inoculation temperature: Beans at roughly 40 to 45°C when adding starter
- Fermentation: 40 to 42°C, 85 to 90% humidity, 18 to 24 hours
- Aging: Refrigerate at least 24 hours before eating, keeps 7 to 14 days