Natto: Japanese Fermented Soybeans
A Probiotic Powerhouse with an Unforgettable Stringy Personality
Natto divides people into two passionate camps: those who adore its funky, umami-rich intensity and those who... don't. There's rarely middle ground with this traditional Japanese breakfast staple. Made from soybeans fermented with Bacillus subtilis, natto develops a distinctive sticky, stringy texture and a pungent aroma that's often compared to aged cheese.
I learned to love natto out of necessity back in 1992, living in a dormitory in the ski fields of Gunma. When it's what's available for breakfast every day, you either make peace with it or go hungry. For about a month, I'll admit I struggled with it - in fact I rejected it - and to the horror of people around me - microwaved the egg and put Kewpie over that and the rice - pretty yum really). Anyway - within a month, after the first few mornings of trying it - I found myself craving that distinctive, almost addictive funk, and the entertaining ritual of stirring it into hot rice, trying to tame those silky strings wrapped around my chopsticks. It's an acquired taste, certainly, but for those willing to embrace the adventure, it becomes addictive.
The reward for stepping outside your comfort zone is that Natto is one of the most nutritious fermented foods on the planet—packed with probiotics, vitamin K2, nattokinase (an enzyme that supports heart health), and highly bioavailable protein. The fermentation process breaks down anti-nutrients in soybeans, making them easier to digest while multiplying their health benefits exponentially.
About Natto
Traditionally eaten for breakfast in Japan, natto is most commonly served over hot rice with a drizzle of soy sauce, a dab of karashi (Japanese mustard), and chopped spring onions. The ritual of stirring natto vigorously to develop those characteristic silky strings is part of the experience—the more you stir, the stringier and creamier it becomes.
Health Benefits:
- Rich in probiotics (Bacillus subtilis) that support gut health
- High in vitamin K2 for bone and cardiovascular health
- Contains nattokinase, an enzyme that may help with blood pressure and circulation
- Excellent source of protein, iron, and calcium
- Easier to digest than unfermented soybeans
Ingredients
For the natto:
- 500g dried soybeans (organic, whole beans—smaller beans produce milder natto)
- 1 packet Natto Starter (or!! just like yoghurt you can backslop - using 2-3 tablespoons store-bought natto as starter)
- 10ml cooled boiled water (if using natto starter powder)
Equipment:
- Pressure cooker or large pot
- Sterilized shallow containers (glass or ceramic, not metal)
- Yogurt maker, Instant Pot with yogurt function, or oven with proof setting
- Paper towel or breathable cloth
- Thermometer (optional but helpful)
Method
Day 1: Soak & Cook
- Soak the soybeans: Rinse soybeans thoroughly in cold water, rubbing gently to remove any dirt. Place in a large bowl and cover with plenty of water (beans will triple in size). Soak for 9-12 hours or overnight. Cover with a cloth.
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Cook until tender: Drain the soaked beans. Cook using one of these methods:
- Pressure cooker: Cover beans with fresh water and cook on high pressure for 30 minutes, or until beans are very soft and can be easily squashed between your fingers.
- Stovetop: Cover with water in a large pot and simmer for 2-3 hours until tender but not mushy. Check water level regularly.
- Sterilize everything: While beans are cooking, sterilize your containers, utensils, and work surface with boiling water. This step is crucial—you want only the right bacteria to thrive.
Inoculation (Work Quickly!)
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Prepare starter solution:
- If using natto starter powder: Dissolve The Fermentary Natto Starter in 10ml cooled boiled water.
- If using store-bought natto: Have 2-3 tablespoons ready (about ⅓ cup).
- Inoculate while hot: Drain the cooked beans immediately (don't let them cool!). Working quickly while beans are still hot (above 70°C), either pour the starter solution over beans and mix thoroughly, OR stir through the store-bought natto until evenly distributed. Speed is essential here—the heat helps prevent contamination.
Fermentation
- Prepare containers: Spread the inoculated beans in a shallow layer (no more than 2-3cm deep) in your sterilized containers. Shallow layers ferment more evenly.
- Cover for airflow: Place a clean cloth over the beans, leaving air circulation. Do NOT seal with a lid—natto bacteria need oxygen to work their magic.
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Maintain warmth: Keep beans at 38-42°C (100-108°F) for 22-24 hours using one of these methods:
- Yogurt maker: Place container inside on yogurt setting
- Instant Pot: Use yogurt function, place container on steam rack with small amount of water beneath (don't submerge)
- Oven: Use proof setting, or preheat to 50°C, turn off, and place beans inside with oven light on
- Dehydrator: Set to 40°C if your model accommodates containers
- Monitor: Check after 18 hours. You should see white film developing on beans and notice that distinctive natto aroma. If beans look dry, they may need a few more hours. After 24 hours, natto should be sticky and stringy when stirred.
Maturation
- Rest in fridge: Transfer containers to the refrigerator immediately and let them mature for at least 12-24 hours before eating. This secondary fermentation reduces the ammonia smell, develops flavor complexity, and increases amino acid content.
How to Enjoy Natto
Traditional style:
- Serve over hot rice
- Add soy sauce and karashi (Japanese mustard)
- Top with chopped spring onions, nori strips, or bonito flakes
- Stir vigorously 50-100 times to develop maximum stringiness!
- Natto with raw egg yolk, soy sauce, and wasabi
- Natto sushi rolls - great for roll your own sushi night
- Natto pasta (surprisingly delicious!)
- Mixed with grated horseradish and microgreens
If you're a natto newbie, try:
- Mixing with kimchi to mask the intensity
- Adding to scrambled eggs or omelettes
- Stirring into miso soup
- Incorporating into fried rice (the heat mellows the flavor)
- Spreading on avocado toast with sesame oil
- Mixing with grated daikon and soy sauce
- Adding to okonomiyaki batter (see our okonomiyaki recipe!)
Storage
Refrigerator: Fresh natto keeps for 5-7 days in an airtight container. Flavor improves after 1-3 days of aging.
Freezer: Portion into small containers and freeze for up to 1-2 years. Thaw overnight in the refrigerator.
Perpetual batches: You can use ⅓ cup of your homemade natto as starter for your next batch (instead of commercial starter). This works for up to 3 generations before the bacteria loses potency.
Troubleshooting
Problem: Beans smell strongly of ammonia
Solution: Over-fermented. Next time, check earlier or reduce temperature slightly. The fridge rest will mellow the smell.
Problem: Not enough strings/stickiness
Solution: Fermentation time was too short, temperature too low, or beans were too dry. Stir vigorously—this helps develop strings!
Problem: Strange off-smell or unexpected colors
Solution: Contamination occurred. Discard batch and sterilize everything more thoroughly next time.
What's normal: A soft whitish fuzz on beans, a cheese-like aroma, and that distinctive fermented smell are all perfectly normal!
Tips for Success
- Use smaller soybeans (natto soybeans) if available—they produce milder, more traditional natto
- Fresh homemade natto tastes better and smells milder than store-bought due to better temperature control
- Beginners can use more starter than the recipe calls for—it increases success rates
- Don't skip the refrigerator rest—it genuinely improves flavor
- Stirring natto just before eating develops the best texture
Why Make Your Own?
Commercially produced natto usually comes in styrofoam packaging. Plus - whilst they are a little larger - we have great GMO free, organic soy beans here in Australia. And it's easy!!
Yield
500g dried soybeans makes approximately 1.2kg fresh natto (enough for 15-20 servings)
Get started: Shop The Fermentary Natto Starter—professionally cultured Bacillus subtilis specifically formulated for home natto making. One packet makes multiple batches. Available in our online shop alongside organic soybeans.
There is a more comprehensive story and recipe in my book Ferment for Good.
