How to Make Natto at Home

Table of Contents

1. What Natto Is
2. Equipment and Ingredients
3. The Step-by-Step Home Method
4. Why It Gets Sticky: The Threads
5. Troubleshooting a Batch
6. Food Safety: Spores, Contaminants and When to Discard
7. What Fermentation Changes Nutritionally
8. How to Eat It and How to Store It
9. Who Should Be Careful
10. Key Research Papers
11. Connections
12. Featured Videos

What Natto Is

Natto is a traditional Japanese food made by fermenting whole cooked soybeans with a single bacterium, Bacillus subtilis var. natto. A 2022 critical review of natto science sums up the process in one sentence: soybeans are soaked, steamed or cooked, inoculated with the bacteria, and left to incubate. That is genuinely all there is to it — no salt brine, no months of ageing, no special moulds.

What comes out is unlike any other soy food. The beans turn a deeper yellow-brown, soften, and become coated in a web of fine, stretchy threads. The smell is strong and earthy (some say cheesy, some say like a ripe washed-rind cheese), and the flavour is savoury and nutty. If you have never eaten it, our acquired-taste tips are worth a look before your first batch.

It helps to know where natto sits among soy foods. The site's whole-food doctrine treats fermented soy — natto, miso, tempeh, traditionally brewed soy sauce — very differently from unfermented, industrial soy products such as soy protein isolate, soy milk or soybean oil. Natto is the whole bean, cooked and then transformed by a living culture over a day or more. The fermentation is the point: it is what produces the vitamin K2, the nattokinase and the improved digestibility described further down.

Think of the bacterium as a tiny, tireless cook. Its spores survive boiling, wake up on warm cooked beans, and spend the next day digesting protein, spinning threads and making vitamins. Your job is simply to give it a clean, warm, humid kitchen and keep competitors out.

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Equipment and Ingredients

You do not need a laboratory. You do need a way to hold the beans warm for a full day, because temperature is the single variable that most often makes or breaks home natto.

Ingredients

• Whole dried soybeans. Small-seeded varieties are traditional because more surface area means more threads per bite, but any whole soybean works. Buy whole dried beans — not soy flour, not defatted grits.
• A starter. Either a commercial natto spore powder (sold as a dry culture of B. subtilis var. natto), or a spoonful of plain, fresh store-bought natto. The live bacteria in finished natto will happily colonise a new batch.
• Clean water, for soaking and for dissolving the starter.

Equipment

• A large pot with a steaming basket, or a pressure cooker. A pressure cooker is faster and gives very soft beans.
• Shallow containers — glass or stainless baking dishes work well. Spread the beans no more than about 3 cm deep so air and warmth reach every bean.
• A warm place you can hold near 40 °C (104 °F): a yogurt maker with a large chamber, a dehydrator with a temperature dial, an oven with a proofing setting, or a picnic cooler with a seed-starting heat mat. Whatever you use, check it with a thermometer first.
• A probe thermometer. Guessing the temperature is the most common cause of a failed batch.
• Cloth, paper towel or perforated foil to cover the dish: the culture needs some oxygen and high humidity, but not a pool of condensation dripping onto the beans.
• A clean spoon and boiling water to scald everything that touches the beans after cooking.

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The Step-by-Step Home Method

The method below follows the steps described in the food-science literature. The 2022 critical review describes washing and soaking whole soybeans overnight, cooling the cooked beans to about 45 °C before inoculating, and then fermenting for 18–20 hours at 40–45 °C; it describes the classic stringy style as cultured for 24 hours. A 2026 laboratory comparison soaked beans for 8 hours, steamed them at 105 °C for 90 minutes, fermented at 37 °C for 24 hours and then ripened the natto at 4 °C for 24 hours. Home cooks land in the same window: a 12–18 hour soak, around 40 °C (104 °F), and roughly 18–24 hours of warmth.

1. Wash and soak (12–18 hours). Rinse the dried soybeans until the water runs clear, pick out any split or discoloured beans, and cover with about three times their volume of cool water. They will roughly double or triple in size. Soak overnight — 12 to 18 hours is a good home range. A bean is ready when it splits easily into two halves with no hard, opaque core. In warm kitchens, soak in the fridge or change the water once so the soak itself does not start fermenting.
2. Steam or pressure-cook until very soft. Drain the beans. Steaming keeps them drier than boiling, which the culture prefers. The beans are done when you can squash one easily between thumb and ring finger. In a pressure cooker this takes far less time than steaming in an open pot; in a plain steamer it can take several hours. The 2026 laboratory study steamed at 105 °C for 90 minutes. Under-cooked beans are the second most common cause of failure: the bacterium cannot work its way into a firm bean.
3. Scald your tools, then inoculate while the beans are hot. Pour boiling water over the dish, spoon and anything else that will touch the beans. Drain the cooked beans well and, while they are still hot — around 45 °C (113 °F), the inoculation temperature in the review — sprinkle on the starter. With spore powder, follow the packet's ratio (usually a tiny measuring spoon dissolved in a little boiled, cooled water). With store natto, stir one heaped tablespoon of it into a few spoonfuls of boiled, cooled water and mix that through the beans. Inoculating hot beans gives the natto culture a head start before anything else from the air can settle.
4. Ferment at about 40 °C (104 °F) for 18–24 hours, humid. Spread the beans in a shallow layer, cover loosely with a damp cloth or perforated foil, and hold them warm. Check the temperature in the first hour and again later; heat mats and ovens drift. Around 18 hours you will see a whitish-grey bloom over the beans and smell a strong, nutty aroma; by about 22–24 hours most batches have plenty of threads.
5. Ripen in the fridge for 1–2 days. Cover the dish and refrigerate. This cold rest is not optional decoration: in the 2026 comparison, a 24-hour ripening at 4 °C deepened the flavour and nattokinase activity kept rising. It also mellows the sharp smell of fresh natto.
6. Stir to develop the threads, then eat. Just before serving, stir a portion vigorously with chopsticks — 30 or more strokes — until it foams and the strings turn white and thick. That is the sticky polymer being drawn out, explained in the next section.

Keep back one spoonful from a good batch as the starter for the next one. Many home makers carry a culture forward this way for many generations; if a batch ever turns weak or off, go back to fresh spore powder.

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Why It Gets Sticky: The Threads

The famous strings are made of poly-γ-glutamic acid (often shortened to γ-PGA), a long chain built from the amino acid glutamic acid. Bacillus subtilis and related Bacillus species make it with a dedicated set of genes (the pgsBCA cluster) and also carry a gene to break it back down, according to a 2017 review of γ-PGA biology. The same review describes γ-PGA as biodegradable, biocompatible and non-toxic, which is why industry now uses it in foods, cosmetics and medicines.

A useful picture: the bacterium is weaving a protective net around itself on the surface of each bean. More bacterial growth means more net. That is why the threads are your best quality signal. Plenty of long, white, elastic strings means the natto culture dominated; few or no strings means it struggled — and something else may have taken its place.

Stirring matters because the polymer is tangled and partly collapsed in the fridge. Whipping it with chopsticks stretches the chains and traps air, turning it from a gluey film into a light, foamy web. The 2026 laboratory comparison measured exactly this change in texture: hardness fell during fermentation while viscosity and elasticity rose significantly.

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Troubleshooting a Batch

Most failures trace back to temperature, under-cooked beans or a weak starter. These are cooks' observations, not laboratory findings, but they match the biology above.

• Strong ammonia smell (like window cleaner). The batch has over-fermented: it was held too long or too hot, and the bacteria broke protein down past the savoury stage. A faint whiff that fades after a day in the fridge is normal. An eye-watering smell, a slimy wet texture or very dark, mushy beans means it went too far — compost it and shorten the time or lower the heat next time.
• No strings, or only a few. Usually too cool (below about 37 °C), beans too wet, beans under-cooked, or a starter that was too old or too little. Check your warm box with a thermometer, drain the beans better, and use fresh spore powder. A stringless batch that smells sour, rotten or “off” rather than nutty should be discarded, because it means something other than the natto culture grew.
• Beans dried out and hard on top. Humidity was too low. Use a damp cloth over the dish, or put a small bowl of hot water in the warm box.
• A thin grey-white film over the beans. This is normal — it is the natto bacterium itself.
• Fuzzy mould or coloured spots. Fuzzy growth that is green, blue-green, black, pink, red, orange or yellow means mould or another organism has grown. Discard the whole batch; do not scrape off the spots, because what you see is the visible tip of growth throughout the beans.

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Food Safety: Spores, Contaminants and When to Discard

Why spores matter

Bacillus subtilis is a spore-former. Its spores survive boiling, which is exactly why natto works: the spores ride through the cooking and then germinate on the warm beans. The catch is that a close relative, Bacillus cereus, is also a spore-former, also lives in soil and on dried beans and grains, and also loves warm, moist, protein-rich food. Some strains make toxins that cause vomiting or diarrhoea. Cooking alone therefore does not make the beans sterile; it simply clears the field for whichever Bacillus gets established first. See our Bacillus cereus page for the illness itself.

What the evidence shows

A Korean survey of 162 traditionally fermented soybean products found B. cereus in 110 samples (67.9%), including 18 of 25 cheonggukjang samples (72.0%) — cheonggukjang is a short Korean ferment made with Bacillus, close to natto. Yet a non-hemolytic enterotoxin was detected in only 22 of the 162 samples (13.6%), and the authors concluded that the real risk of illness was lower than generally presumed, while recommending ongoing monitoring (survey, observational).

The reason a strong natto culture helps is competition. A Bacillus subtilis strain isolated from a traditional Korean fermented soybean food inhibited the growth of B. cereus and suppressed its toxin-related genes, and water extracts of soybeans fermented with that strain did the same (laboratory study, one strain — it shows the mechanism, not a guarantee for every home batch). In practical terms: a fast, vigorous fermentation with plenty of starter, at the right temperature, leaves little room for anything else. A slow, lukewarm, weakly inoculated batch is the one that gives competitors a chance.

Rules that keep home natto safe

• Scald every tool, dish and spoon that touches the beans after cooking.
• Inoculate generously and while the beans are hot; do not let cooked beans sit at room temperature before inoculating.
• Hold a steady fermentation temperature — a thermometer is a safety tool here, not a gadget.
• Refrigerate promptly once fermentation ends.
• Discard any batch with coloured or fuzzy mould, a sour or putrid smell instead of a nutty one, no strings at all after a full fermentation, or a slimy, wet, collapsed texture.
• When in doubt, throw it out. A pound of soybeans costs far less than a day of food poisoning.

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What Fermentation Changes Nutritionally

Cooking a soybean already does a great deal: the heat destroys most of its trypsin inhibitors and makes the protein digestible. Fermentation then adds things that plain cooked soybeans simply do not have, and removes a little more of what blocks mineral absorption.

Vitamin K2 (MK-7) appears

Plain soybeans contain essentially no vitamin K2; the natto bacterium makes it, almost all as menaquinone-7 (MK-7). In a Maastricht food study, a meal of 200 g of natto supplied 3.1 micromoles of vitamin K2, and the K2 levels in volunteers' blood afterwards were about 10 times higher than the K1 levels after a matched amount of K1 from spinach (small human feeding study, 6 volunteers). A 2022 review notes natto contains roughly 100 times more MK-7 than most cheeses. The 2026 laboratory comparison found vitamin K2 kept increasing through both fermentation and fridge ripening — one more reason not to skip the cold rest. MK-7 also lingers in the blood far longer than vitamin K1: a 2007 trial found it built up to 7–8 times higher levels with daily intake. That long half-life is what makes natto matter for bone and arterial health — and what makes it a problem with warfarin (see below). More on K2: Natto for Vitamin K2 (MK-7).

Nattokinase is produced

Nattokinase is a protein-digesting enzyme that also breaks down fibrin, the mesh in blood clots. It was named in 1987, when researchers measured a strong fibrin-dissolving activity in natto averaging about 40 plasmin units per gram of wet natto (laboratory study). Cooked soybeans have none. In the 2026 comparison, nattokinase activity rose through fermentation and kept rising during ripening. Whether eating natto dissolves clots in people is a separate question covered on the nattokinase and fibrinolysis page; nattokinase is destroyed by high heat, so add natto to food at the end rather than cooking it hard.

Phytic acid falls; trypsin inhibitors mostly fell already

Phytic acid binds iron, zinc and calcium in the gut. A study optimising kinema — a Bacillus-fermented soybean food from the eastern Himalaya, made much like natto — found that soaking and cooking each lowered phytic acid, and fermentation lowered it further; overall, phytic acid fell 61% and trypsin-inhibitor activity 71% compared with raw beans (laboratory study). Importantly, in that study the trypsin inhibitors were cut by soaking and cooking, and fermentation itself left them unchanged. So the honest summary is: cook your beans thoroughly, and let the fermentation take phytate down further. The same principle is explained for grains and seeds on our soaking, sprouting and fermenting page.

Protein becomes easier to digest

The natto bacterium secretes enzymes that pre-digest soy protein. In the 2026 comparison, water-soluble protein kept increasing and free amino acids surged after fermentation, isoflavones shifted toward the more easily absorbed aglycone form, and GABA rose (laboratory analysis of one strain). Fat and sugars fell slightly, because the bacteria use them as fuel. The 2022 review likewise credits heat denaturation, trypsin-inhibitor loss and bacterial breakdown of protein into easily digested peptides for natto's improved nutritional value. For the full nutrient profile per serving, see Natto Nutrients.

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How to Eat It and How to Store It

The classic bowl

The traditional way is simple: stir the natto until stringy, season it, and pour it over a bowl of hot rice. On this site we suggest brown rice, which keeps the bran and its fibre and minerals. Classic toppings:

• Hot mustard (Japanese karashi) — a small dab cuts the earthy smell.
• Sliced scallion — fresh, sharp and green.
• Traditionally brewed soy sauce — a fermented soy food in its own right; a few drops is enough.
• A raw egg yolk — makes the bowl silky and rich. Raw or undercooked shell eggs carry a real risk of Salmonella Enteritidis infection, which the CDC has linked to repeated outbreaks. Use very fresh eggs from a trusted source, kept cold, or pasteurised-in-shell eggs; anyone pregnant, very young, elderly or immune-compromised should skip the raw egg or use a softly cooked one. More on choosing eggs: Eggs.

Other good homes for natto: folded into an omelette at the end of cooking, spooned on avocado or kimchi, mixed with grated daikon, or stirred into miso soup just before serving. Because nattokinase is heat-sensitive, add it last rather than simmering it.

Storage

• Fridge: about one week in a covered container. The flavour strengthens and the ammonia note grows with time, so eat the batch early.
• Freezer: natto freezes well. Portion it into small containers or a flat bag before freezing, then thaw a portion overnight in the fridge. Many home makers freeze most of each batch the day after ripening and keep one container in the fridge.
• Keep a starter: freeze a spoonful from your best batch to inoculate the next one.

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Who Should Be Careful

Natto is a food eaten daily by millions, but a few groups need to know these documented risks before making or eating it.

• People taking warfarin. Warfarin works by opposing vitamin K, and natto is one of the richest vitamin K2 foods known. Researchers developing a special low-MK-7 natto state plainly that ordinary natto must be avoided by warfarin-dependent patients; their low-MK-7 version, at 20 g a day (46 micrograms of MK-7), did not change INR in a 10-patient trial. A 2007 study warned that as little as 50 micrograms a day of MK-7 may interfere with oral anticoagulants in a clinically relevant way. If you take warfarin, do not start eating natto without your prescriber. The newer anticoagulants do not work through vitamin K, but nattokinase may add to bleeding risk with any blood thinner — see Natto Safety and Interactions.
• Soy and natto allergy. Anyone allergic to soy should avoid natto. Natto also causes a distinctive delayed allergy: in a review of 7 patients, reactions including hives, breathing difficulty and loss of consciousness began 5 to 14 hours after eating natto (case series). Several reports link this to sensitisation to γ-PGA, the sticky polymer itself. More: Food Allergy.
• Seriously ill or immune-compromised people. The natto bacterium is generally regarded as safe, but it can rarely enter the bloodstream. In one Japanese hospital, 69 of 70 B. subtilis blood isolates over seven years were the natto strain; patients were mostly elderly (median age 79), and 16% of those with true bacteremia died within 30 days (retrospective cohort). A 2026 case series described three more cases, all in people with impaired gut barriers or immunity (dialysis, late pregnancy, an undiagnosed colon cancer). This does not make natto dangerous for healthy people, but people on dialysis, with active cancer, or recovering from major gut surgery should talk with their care team.
• Raw egg eaters at higher risk — pregnant people, young children, older adults — should leave out the raw egg topping, as noted above.

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Key Research Papers

1. Afzaal M, Saeed F, Islam F, Ateeq H, Asghar A, Shah YA, Ofoedu CE, Chacha JS (2022). Nutritional Health Perspective of Natto: A Critical Review. Biochem Res Int. — PubMed PMID: 36312453
2. He Y, Jiang Y, Li D, Ou X, Miao X, Sun M, Niu H, Hua M, Su Y, Wang J, Liu Z (2026). Differences in Nutrition and Sensory Quality Between Cooked Soybeans, Fermented Natto, and Post-Ripening Natto. Foods. — PubMed PMID: 41596835
3. Sumi H, Hamada H, Tsushima H, Mihara H, Muraki H (1987). A novel fibrinolytic enzyme (nattokinase) in the vegetable cheese Natto; a typical and popular soybean food in the Japanese diet. Experientia. — PubMed PMID: 3478223
4. Schurgers LJ, Vermeer C (2000). Determination of phylloquinone and menaquinones in food. Effect of food matrix on circulating vitamin K concentrations. Haemostasis. — PubMed PMID: 11356998
5. Schurgers LJ, Teunissen KJ, Hamulyák K, Knapen MH, Vik H, Vermeer C (2007). Vitamin K-containing dietary supplements: comparison of synthetic vitamin K1 and natto-derived menaquinone-7. Blood. — PubMed PMID: 17158229
6. Sharma A, Kumari S, Wongputtisin P, Nout MJ, Sarkar PK (2015). Optimization of soybean processing into kinema, a Bacillus-fermented alkaline food, with respect to a minimum level of antinutrients. J Appl Microbiol. — PubMed PMID: 25882160
7. Hsueh YH, Huang KY, Kunene SC, Lee TY (2017). Poly-γ-glutamic Acid Synthesis, Gene Regulation, Phylogenetic Relationships, and Role in Fermentation. Int J Mol Sci. — PubMed PMID: 29215550
8. Kim CW, Cho SH, Kang SH, Park YB, Yoon MH, Lee JB, No WS, Kim JB (2015). Prevalence, genetic diversity, and antibiotic resistance of Bacillus cereus isolated from Korean fermented soybean products. J Food Sci. — PubMed PMID: 25472031
9. Eom JS, Lee SY, Choi HS (2014). Bacillus subtilis HJ18-4 from traditional fermented soybean food inhibits Bacillus cereus growth and toxin-related genes. J Food Sci. — PubMed PMID: 25359543
10. Nakajima T, Taya Y, Nishikawa T, Kitamura Y, Kato H, Mathis BJ, Hiramatsu Y (2021). First Clinical Trial of a Newly Developed, Low Menaquinone-7, Fermented Soybean Natto in Warfarin-Dependent Patients. J Med Food. — PubMed PMID: 34406879
11. Inomata N, Osuna H, Kawano K, Yamaguchi J, Yanagimachi M, Matsukura S, Ikezawa Z (2007). Late-onset anaphylaxis after ingestion of Bacillus Subtilis-fermented soybeans (Natto): clinical review of 7 patients. Allergol Int. — PubMed PMID: 17519580
12. Sada RM, Yamamoto G, Hamaguchi S, Kuroda E, Okura A, Cai M, Nakanishi K, Abe N, Yamamoto S, Kutsuna S (2025). The Majority of Bacillus subtilis Strains Isolated From Blood Cultures Were Derived From Traditional Japanese Fermented Soybeans Natto: A Single-center Retrospective Study. Open Forum Infect Dis. — PubMed PMID: 41018695
13. Ishizawa H, Oshima T, Yara N, Miyasato H, Kuriyama Y, Murakami T, Okura A, Yamamoto G, Kutsuna S, Narita M (2026). Bacillus subtilis var. natto bacteremia: A case series and review. IDCases. — PubMed PMID: 42569355
14. Centers for Disease Control and Prevention (2000). Outbreaks of Salmonella serotype enteritidis infection associated with eating raw or undercooked shell eggs — United States, 1996–1998. MMWR Morb Mortal Wkly Rep. — PubMed PMID: 10706440

PubMed Topic Searches

1. PubMed: Natto fermentation with Bacillus subtilis
2. PubMed: Bacillus cereus in fermented soybean foods
3. PubMed: Antinutrients in fermented soybeans

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Connections

• All Food
• Natto
• Fermented Foods
• Natto Nutrients
• Natto for Vitamin K2 (MK-7)
• Natto: Acquired-Taste Tips
• Natto Safety and Interactions
• Bacillus Subtilis and Gut Health
• Nattokinase
• Vitamin K2
• Bacillus subtilis
• Bacillus subtilis in Natto
• Bacillus cereus
• Food Allergy
• Brown Rice
• Soaking, Sprouting and Fermenting

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