Before you make natto it is important that all utensils that come into contact with the natto starter or soybeans are as sterile as possible, for example by boiling them for 10 minutes. You should take care to avoid any skin contact with product. Below instructions will give you 1 kg finished natto.
The best is to use the typical very small natto soybeans. Soak the soybeans for 12 hours (up to 24 hours longer in colder climates) in 3 liters water. Drain the beans and place them in a large pot. Fill with water and boil for 8 hours or until the soybeans are soft. Alternatively you can cook (or even better steam) the soybeans in a pressure cooker during 45 minutes at max. pressure.
Quickly drain the cooked beans and place the moist and steaming beans in a sterilized pot. When the beans are still very hot (around 80°C) add 1 g natto starter (about 1/4 teaspoon) and stir very well with a clean spoon. Adding the natto starter while the beans are still very hot is important because the heat chock will germinate the bacillus spores and at the same time unwanted bacteria are killed. Put a layer of soybeans in the glass containers. Allow the temperature to drop to about 40°C (104 °F), place the sterilized cheese cloth over the containers and place the lid over the cheese cloth. Place the containers in the incubator or oven set at 40°C during 8 to 12 hours. After this period the beans should be covered with bacillus bacteria (long threads are visible if you stir the beans with a stick) and the typical natto taste should be noticeable. You can incubate the natto a bit longer if you prefer a stronger taste and aroma.
When the natto is finished it should be stored in the refrigerator. You can eat the natto immediately but the quality will improve if you store it in the refrigerator for a few days.