Timeline at a glance
- Day 1 evening: Soak soybeans 12–24 hours
- Day 2: Pressure-cook 45 min → cool to 45°C → inoculate → start fermentation
- Day 2–3: Ferment at 40–45°C for 22–24 hours
- Day 3: Refrigerate for minimum 24 hours to mature
- Day 4: Eat. Total active time: ~1 hour.
Choose your heat source
- Instant Pot (yogurt mode): yogurt mode typically holds 40–43°C — ideal for natto. The easiest option. Prop the lid ajar with a chopstick for airflow.
- Oven with light on: many ovens hold 40–46°C with just the light bulb. Test yours with a thermometer before committing beans.
- Insulated cooler + hot water bottles: fill two bottles with 50°C water, place in a cooler with the beans, replace every 8–10 hours. Low-tech but reliable.
- Dehydrator set to 40°C: works well for small batches if your dehydrator has a temperature dial that goes low enough.
- Natto maker: a dedicated device (~$30–60) with thermostat control. Eliminates temperature guesswork for regular batchers.
The biology is the same regardless of method: Bacillus subtilis natto needs 40–45°C and some airflow. Verify your setup holds temperature before starting.
What You Need: Ingredients and Equipment
Ingredients
- 150g dried soybeans (small to medium size, not split). Small soybeans ferment more evenly than large ones. Yields roughly 350g cooked beans — enough for 3–4 servings.
- Natto starter: 0.1g powdered Bacillus subtilis natto spores per 150g dry beans, OR 1 tablespoon fresh store-bought natto mixed with 1 tablespoon warm water. GEM Cultures, Natural Import Company, and several Amazon sellers carry powdered natto starter.
Equipment
- Pressure cooker or large pot — pressure cooking (45 minutes at high pressure) produces the best texture. Stovetop boiling works but takes 3–4 hours.
- Shallow container with ventilation — the beans need airflow. A glass or plastic container with the lid slightly cracked, or poke 10–15 small holes in the lid.
- Probe thermometer — essential for verifying your incubation setup. The 40–45°C window is narrow; guessing by touch is unreliable.
Find natto starter (Bacillus subtilis) on Amazon →
Find a dedicated natto maker on Amazon →
Step 1 — Soak the Soybeans (12–24 Hours)
Rinse 150g dried soybeans under cold water. Place in a large bowl and cover with at least 3x their volume in cold water — the beans will double or triple in size. Soak for 12–24 hours at room temperature. In summer (above 25°C), soak in the refrigerator to prevent unwanted fermentation.
The beans are ready when you can split one cleanly between your fingers with no hard white core in the center. Under-soaked beans cook unevenly and produce patchy fermentation.
Step 2 — Cook Until Easily Crushable
The beans must be soft enough to crush between two fingers with almost no resistance. This is softer than you expect — most first-batch failures come from under-cooking.
- Pressure cooker: 45 minutes at high pressure, natural release. This is the recommended method — faster and more consistent. For the Instant Pot: add beans and enough water to cover by 3cm, seal, High Pressure 45 min, natural pressure release.
- Stovetop boiling: 3–4 hours at a steady simmer, adding water as needed to keep beans submerged. Skim foam periodically.
Test by pressing a bean between your thumb and finger. It should crush easily into paste with no gritty or firm center. If in doubt, cook longer — over-cooked is better than under-cooked for natto.
Step 3 — Inoculate With Starter at 45°C
Drain the cooked beans thoroughly. While the beans are still hot (around 70–80°C), work quickly — the heat helps sterilize the surface, reducing competition from other bacteria.
- Dissolve the starter: mix 0.1g powdered natto starter with 2 tablespoons of warm (40°C) boiled water. Or mash 1 tablespoon of store-bought natto with 1 tablespoon warm water until the liquid is cloudy.
- Let beans cool to 45°C before adding the starter. Above 50°C kills Bacillus subtilis. Use a probe thermometer.
- Pour the starter liquid over the beans and stir gently to distribute evenly. Every bean should have contact with the inoculated liquid.
- Spread beans in a thin layer (2–3cm deep) in your container. Cover with a lid that allows airflow — leave the lid ajar, or use a lid with holes punched in it. Bacillus subtilis is aerobic and needs oxygen to grow.
Ventilation is the most overlooked requirement. Without airflow, condensation forms on the lid and drips onto the beans, creating soggy patches where the bacteria cannot colonize.
Step 4 — Ferment at 40–45°C for 22–24 Hours
Place the container in your chosen heat source and maintain 40–45°C for 22–24 hours. The temperature window matters:
- Below 38°C: Bacillus subtilis growth slows dramatically. Fermentation may take 30+ hours and produce weak strings.
- 40–45°C: optimal range. Strong bacterial growth, good string formation, balanced flavor.
- Above 50°C: the bacteria begin to die. A short spike is survivable, but sustained heat above 50°C kills the culture.
Check temperature every 8 hours. If using hot water bottles, replace them when the temperature drops below 38°C.
Signs of progress during fermentation
- Hours 6–10: beans develop a faint earthy smell. No visible change yet.
- Hours 12–16: white film begins to appear on bean surfaces. A mild ammonia smell is normal.
- Hours 20–24: beans are covered in a thin white coating. When stirred, sticky strings form between the beans. The ammonia smell is present but not overwhelming.
Instant Pot Method (One-Vessel Approach)
The Instant Pot handles both the cooking and fermentation stages without extra equipment:
- Add soaked soybeans and enough water to cover by 3cm. Seal the lid. Set to High Pressure for 45 minutes, then natural pressure release.
- Open the lid, drain excess water, and let beans cool uncovered in the pot until they reach 45°C.
- Add inoculant, stir gently, and spread beans evenly in the pot.
- Place a chopstick under the lid to create a 1–2mm gap for airflow. Switch to Yogurt mode (Normal setting), which holds approximately 40–43°C.
- Ferment for 22–24 hours. Check at 12 hours — the white film should be starting to form.
The slight temperature variation between Instant Pot yogurt mode models (some run at 40°C, some at 43°C) is within the acceptable window. Both produce reliable natto.
Step 5 — Refrigerate for 24 Hours to Mature
Transfer the container to the refrigerator, sealed, for at least 24 hours before eating. This maturation step is not optional — it allows the flavor to mellow, the ammonia to dissipate, and the texture to firm up. Natto eaten directly after fermentation is harsh and overly pungent.
After 24 hours of refrigeration, stir with chopsticks. You should see long, sticky strings stretching between the beans — this is polyglutamic acid and confirms successful fermentation.
How to Make Natto Taste Good: Serving and Preparation
The texture and smell of natto are the primary barriers for new eaters. These techniques help:
- Stir vigorously before seasoning: use chopsticks and stir 30–60 times before adding anything. Agitation creates a frothy, lighter texture and develops more strings. The aggressive stirring also subtly changes the flavor — more mellow and less harsh.
- Classic condiments: Japanese mustard (karashi) + soy sauce or tsuyu. The mustard cuts the heavy fermented flavor. Start with a small amount.
- Serve over very hot rice: the heat from the rice warms the natto slightly and softens the flavor. The contrast of sticky natto and fluffy rice is the canonical combination.
- Additions that mellow natto: thinly sliced green onion (negi), grated daikon, a raw egg yolk, and okra. Each contributes its own stickiness that blends with the natto texture.
- Cooked applications: natto fried rice (fold in after the heat is off), natto tamagoyaki, natto avocado toast, natto in miso soup. Heat breaks down some of the stringiness and mellows the sharp ammonia note for people who find the raw form difficult.
- With kimchi: natto + kimchi + rice is a popular modern combination in Japan — the acidity of kimchi balances the alkaline fermented flavor of natto.
Where to Buy Natto (If You Don't Want to Make It)
Natto is available at Japanese grocery stores (Mitsuwa, Marukai), Korean supermarkets (H Mart), and some Asian grocery chains. Look for it in the frozen section in small styrofoam trays — typically sold as sets of 3 individual trays. Common brands: Shirakiku, Azuma, Okame, and Kinusato (silken natto, milder flavor).
Online: frozen natto ships reliably via Amazon. Nattokinase supplements (the extracted enzyme) are different from whole natto and are sold separately for cardiovascular applications.
For sourcing outside Japan or major US cities: frozen natto ordered online is the most reliable option. Starter spores are more widely available than finished natto in many regions.
Troubleshooting: What Went Wrong and Why
- No strings after 24 hours: temperature was too low (below 38°C), starter was dead, or the beans were contaminated before inoculation. Verify temperature first — this is the most common cause.
- Slimy but no strings: the beans were too wet during fermentation. Condensation from poor ventilation drowns the surface bacteria. Ensure the lid allows airflow and the bean layer is no more than 3cm deep.
- Strong ammonia that does not fade: over-fermented. The fermentation ran too long or too hot. Reduce time to 20 hours on the next batch and keep temperature at 40–42°C.
- Pink, orange, or green discoloration: contamination by unwanted bacteria or mold. Discard the batch. Sterilize your container before the next attempt — wash with boiling water or a no-rinse sanitizer.
- Bitter flavor: usually caused by old or degraded starter, or beans that were under-cooked. Use fresh starter and ensure beans crush easily between fingers before inoculating.
- Beans too firm after fermentation: under-cooked. The bacteria cannot colonize fully if the soybean interior is still starchy and dense. Cook the next batch longer — even 60 minutes at high pressure — and re-test crushability before inoculating.
How Long Does Homemade Natto Keep?
- Refrigerator: 5–7 days in an airtight container. The flavor intensifies over time.
- Freezer: up to 3 months. Portion into individual servings before freezing. Thaw overnight in the refrigerator.
For what natto is, its nutrition profile, and how it fits into the Japanese pantry → What Is Natto. For temperature guidance across different ferments → Fermentation hub.
Frequently asked questions
Why does my natto smell strongly of ammonia?
Mild ammonia is normal and fades after 24 hours of refrigeration. Strong, persistent ammonia means the beans over-fermented — usually because the temperature exceeded 45°C for an extended period or fermentation ran longer than 26 hours. Shorten the fermentation window to 20–22 hours on your next batch and verify temperature with a probe thermometer. Over-fermented natto is still safe to eat but has a harsh, bitter flavor that most people find unpleasant.
Can I use store-bought natto as a starter instead of spore powder?
Yes. Mix 1 tablespoon of fresh store-bought natto with 1 tablespoon of warm (40°C) water, stir to distribute the bacteria, and pour over your cooked soybeans. This works reliably for 2–3 generations — after that, bacterial vigor decreases and you should start from fresh commercial natto or powdered starter. The advantage of powdered Bacillus subtilis natto starter is consistency: each packet has a standardized spore count that produces reliable results batch after batch.
What is the stringy white substance in natto?
The strings are polyglutamic acid (PGA), a natural polymer produced by Bacillus subtilis during fermentation. Stringiness is the primary indicator of successful natto — the longer and stickier the strings when you stir, the more complete the fermentation. If your natto produces no strings after 24 hours, the bacteria did not establish: check that your starter was viable and that the temperature stayed in the 40–45°C range throughout.
How long does homemade natto keep in the refrigerator?
Homemade natto keeps 5–7 days refrigerated in an airtight container. For longer storage, freeze individual portions in small containers or zip-lock bags — frozen natto keeps for 3 months with minimal texture change. Thaw in the refrigerator overnight before eating. The flavor continues to develop (stronger, more pungent) even under refrigeration, so freezing at day 1–2 preserves a milder taste.
Can I make natto without natto starter?
Yes — use 1 tablespoon of fresh store-bought natto (not frozen, not pasteurized) mixed with 1 tablespoon of warm water as your inoculant. The Bacillus subtilis bacteria in commercial natto are still live and viable. This method works reliably for 2–3 generations of home batches. Without any natto or starter at all, you cannot reliably produce natto — the fermentation requires a specific strain of Bacillus subtilis natto, not the wild Bacillus naturally present on rice straw or in the environment.
How do I make natto taste better?
The traditional method: stir vigorously with chopsticks for 30–60 seconds before adding condiments — agitation increases the stickiness and develops a frothy, milder flavor. Then add Japanese mustard (karashi), a splash of soy sauce or tsuyu, and serve over hot rice. Beyond the classic: top with green onion, grated daikon, a raw egg yolk, or kimchi. Natto also mellows significantly when heated — fold it into fried rice or use it in tamagoyaki (rolled egg) if the raw texture is a barrier.
How long does it take to make natto from start to finish?
Total active time is about 1 hour, but the process spans 2–3 days: 12–24 hours soaking, 45 minutes pressure-cooking, 22–24 hours fermentation at 40–45°C, and then at least 24 hours of refrigeration to mature. You eat it on day 3 or 4 from when you started soaking. The fermentation itself (the hands-off time in your heat source) is 22–24 hours. The maturation refrigeration step adds another 24 hours before the flavor is at its best.
Can I make natto in an Instant Pot?
Yes — the Instant Pot handles two stages. Use High Pressure for 45 minutes to cook the soybeans (add water to just cover, natural release). After inoculation, use Yogurt mode (Normal setting, which holds 40–43°C) for the 22–24 hour fermentation. Place a chopstick under the lid to allow airflow — Bacillus subtilis is aerobic and needs some oxygen. This is the easiest home method because you cook and ferment in one vessel with reliable temperature control.
Where can I buy natto near me?
Natto is sold at Japanese grocery stores (Mitsuwa, Marukai, H Mart), Korean supermarkets, and some Whole Foods locations. It is typically in the refrigerator or freezer section in small styrofoam trays, 3 per pack. Frozen natto ships reliably — look for brands like Shirakiku, Azuma, or Okame on Amazon. If you cannot find it locally and do not want to make it, frozen natto ordered online is the practical solution for most people outside major cities.
Can I make natto in India?
Yes — the process is identical. The primary sourcing challenge is natto starter. GEM Cultures ships internationally, and natto starter is available on Amazon India (search 'natto starter bacillus subtilis'). Soybeans are widely available in India. For the heat source, a yogurt maker or a warm oven with the light on (check temperature first with a thermometer) works well in warm climates. Note that in summer months in India, room temperature may be high enough to affect the fermentation — keep the incubation container away from direct heat if ambient temperatures exceed 30°C.
What is nattokinase and should I take it as a supplement?
Nattokinase is a serine protease enzyme produced by Bacillus subtilis natto during fermentation. In laboratory settings, it has demonstrated fibrinolytic (clot-dissolving) activity. Nattokinase supplements are marketed for cardiovascular health. However, the enzyme is largely broken down during digestion, and clinical evidence for cardiovascular benefit in humans is limited and preliminary. If you are on blood-thinning medication (warfarin, aspirin), consult a doctor before taking nattokinase supplements — there are potential interactions. Eating natto as food is generally safe; high-dose supplements require more caution.
Where to go next
- Fermentation hub — the full Japanese fermentation landscape: miso, koji, vinegar, amazake
- What Is Natto — what natto is, nutrition, nattokinase, and its role in Japanese food culture
- Miso vs Shio Koji — adjacent koji-based seasonings: when each is the right tool
- How to Make Rice Vinegar — another home fermentation project: full method, shortcut, and seasoned sushi-zu recipe
- Amazake — koji-fermented sweet rice drink: a gentler fermentation project for beginners
- Okayu — Japanese rice porridge: the classic base for natto gohan, the simplest natto meal format
- What Is Amazake — another fermented rice food: koji-based, no alcohol, a gentle companion ferment to natto