Zero-waste Natto

Updated: Feb 20

Stinky beans or bacillus subtilis (Hay bacillus) fermented soybeans is called natto 納豆 in Japanese. There's a very nice write-up about it on LiveJapan.com that explained its name as possibly originating from “beans for the general” (将軍 に めた ) /Shōgun ni osameta mame/. While its smell is as subjective as durian or blue cheese, it tastes really delicious and most importantly, it is sooooo healthy! Natto has one of the highest vitamin K content (important to prevent blood thrombosis) and the protein dissolving enzyme nattokinase is beneficial in preventing cardiovascular illness and even promoted in reducing endometrial adhesions. Do your own research as well to discover more about the health benefits of natto. I really miss the traditional breakfast in Japan that always has natto and mustard to go with the fluffy fragrant rice. We have natto abundantly in Singapore but unfortunately in single serving portions packed in styrofoam boxes and plastic packs of soy sauce and mustard.

I have been getting my natto fixes at a local Japanese restaurant but I don't know if they make their own natto or if they serve it from those little styrofoam packs. So I plucked up my courage to extend my fermentation repertoire from yogurt, pickled vegetables, kombucha, now to natto.


I have a rough idea of what is possible, without purchasing the bacteria innoculum and so started researching on the internet, and Youtube for that 'see-it-to-believe-it' assurance. My inspiration is Emmymade (hyperlink available by clicking screenshot on the right). I followed her links to other references such as NattoDad; the Obaasan who ferment natto in paper swaddled with blankets (😆 awwww...) and the professional natto master of Kyo-natto to understand more about natto fermentation from various angles.


I bought a pack of commercial natto for innoculum, like Nattodad and Emmy did. It happened to be a super-natto (sugoi) S-903 strain 😂. Check out the super power claims online!




My deviation will be to use whatever I have and omit the plastic shrink wrap. The role of the perforated shrink wrap is not to make it an anaerobic fermentation but rather to slow down loss of moisture during the fermentation. So this is how I made my zerowaste natto:

  1. I soaked a cup of organic soybeans [note 1] in tap water for 8-12 hours. You can soak it in the fridge for 2 days if you want to make sprouted natto.

  2. Wash the soaked beans to remove dirt etc.

  3. Steam the soaked beans till soft or like me, just chuck it in a Crocker pot and boil at auto-heat overnight.

  4. In the morning, check the consistency of the beans. Test on one bean, it should be easily mashed to a paste-like consistency. Turn off the heat, drain the excess liquid into a container for alternative use(s) [note 2] and allow the beans to cool down (with lid covered to prevent avoid contamination) to around 40degC or just warm. [note 3]

  5. Using a stainless steel spoon sterilised with boiling water, scoop about half of the commercial natto in the single serving box (you can empty the whole box if you want, more innoculum, the faster and safer the fermentation). I choose to enjoy the other half instead. Stir in the commercial natto to ensure the innoculum is well distributed.

  6. Using the same plastic film that covered the natto in the commercial pack, I used it instead of the disposable cling wrap, to reduce the evaporation of moisture. Instead of a 2nd barrier of cling wrap, I covered the non-airtight glass lid.

  7. To maintain the temperature, I placed the terracotta crock pot (not the heating element) onto a hot spot on top of my fridge for the day (10 - 16 hours). You can place it in preheated oven set to low heat. If you do want to transfer the beans into another container, ensure it is well sterilised before transfer.

  8. You can add a tablespoon of the boiled soybean water to prevent drying out. As I only drain the liquid from the pot without the use of strainer, the beans were still quite moist so I kept the soybean water in the fridge.


9. Once the fermentation is done, you will see the stringy texture spread throughout the pot. I did not manage to get the white fuzz mentioned by Emmy. Maybe my next try!





10. Further fermentation will release ammonia and stronger odour so slow down the fermentation by putting it in the fridge. Protect it from any lactobacillus culture which can weaken the natto bacteria. Picture on the right is after stirring and hence the bubble. Without stirring, there is no visible bubbles.




Bring along your container / produce bag to buy organic soybeans and try your hand at DIY natto if you like it too!

Note 1: You may use the small natto-beans which will allow the taste to penetrate more thoroughly into the middle. I use the normal organic soybeans. For taste improvement, you can break the beans prior to fermentation known as hikiwari natto . You can even try with red beans, black soybeans, green bean based on the online research I've made. Note 2: Cooked soybean water is said to be good for making clothes whiter. I have not tried it. The water is also rich in umami and nutrients, use as soup stock or fertilize the plants! Note 3: Steaming the soybeans would likely be better in retaining the nutrients and flavour. Do not put the innoculum into steaming hot soybeans as the bacteria will die from excess heat.