Nattokinase is produced during the fermentation of soybeans by the bacterium Bacillus subtilis natto, the same process used to make the traditional Japanese food natto. You don’t synthesize nattokinase separately; you create the conditions for the bacteria to produce it as they ferment the beans. The fermentation itself is straightforward, but getting a high enzyme yield depends on precise temperature, humidity, and pH control.
What Nattokinase Actually Is
Nattokinase is a protein-dissolving enzyme that Bacillus subtilis natto secretes as it feeds on cooked soybeans. The enzyme’s defining property is its ability to break down fibrin, the protein that forms the structural mesh of blood clots. This fibrinolytic activity is measured in fibrinolytic units (FU), and commercial supplements typically contain around 2,000 FU per capsule. When researchers test nattokinase potency, they place measured amounts of the enzyme on fibrin plates and measure the size of the clear zone where the fibrin dissolves.
The enzyme is naturally present in finished natto. Eating natto is the simplest way to consume nattokinase, though the amount varies depending on how the fermentation was carried out.
The Basic Fermentation Process
Making natto (and therefore nattokinase) requires three things: cooked soybeans, Bacillus subtilis natto starter culture, and a warm, humid environment held steady for about 18 to 24 hours.
- Soak the soybeans. Use whole, dried soybeans. Soak them in water for 12 to 24 hours until they’ve roughly doubled in size.
- Cook thoroughly. Steam or pressure-cook the soybeans until they’re soft enough to crush easily between your fingers. Pressure cooking for 45 minutes works well. Boiling also works but can take several hours. The beans must be fully cooked so the bacteria can access the proteins inside.
- Sterilize your equipment. Before inoculating, heat your containers, mixing utensils, and any covering material in an oven at around 120°C (250°F). Contamination by unwanted bacteria is the main safety risk in home fermentation.
- Inoculate while hot. Dissolve a small amount of Bacillus subtilis natto spore powder in warm, sterile water and mix it into the hot soybeans. Work quickly. The residual heat from the beans helps suppress competing microbes. Disinfect any gloves or spoons in hot water before they touch the beans.
- Spread thin. Distribute the inoculated beans in shallow containers, no more than a few centimeters deep. The bacteria need oxygen, so the beans shouldn’t be packed tightly. Cover with perforated plastic wrap or breathable cloth.
- Ferment. Hold the beans at approximately 39 to 40°C (102 to 104°F) and 90% relative humidity for 18 to 24 hours. A standard approach from research is 39°C for 18 hours at 90% humidity, followed by a 2-hour cooldown at 20°C and 50% humidity. Home fermenters often use an oven with the light on, a food dehydrator set to low, or a cooler with a reptile heat mat and a small dish of water for humidity.
- Cool and rest. After fermentation, refrigerate the natto for at least several hours. This aging step allows flavor development and continued enzyme activity at a slower rate.
When done correctly, the beans will be covered in sticky, stringy threads when you pull them apart. Some ammonia smell is normal. If the smell is overwhelmingly strong, unwanted bacteria may have taken over, and you should discard the batch.
Conditions That Maximize Enzyme Yield
Not all natto contains the same amount of nattokinase. The enzyme yield depends heavily on temperature, pH, and the nutrients available to the bacteria. Research on optimizing nattokinase production has found that 37°C is the ideal temperature for maximum enzyme activity, and a pH of 8 (slightly alkaline) produces the highest yield. In one optimization study, the best conditions produced enzyme activity of 3,770 FU/mL, a dramatically higher output than unoptimized fermentation.
For home production, you can’t easily control pH the way a lab does, but you can focus on what’s within your reach: maintaining a steady temperature between 37 and 40°C, keeping humidity high, ensuring the beans are spread thin enough for oxygen exposure, and using a quality starter culture. Temperature swings are the most common reason for low enzyme output or failed batches.
Choosing a Starter Culture
You have two options for introducing the bacteria: purchased Bacillus subtilis natto spore powder, or a spoonful of store-bought natto. Spore powder is the better choice. It’s more economical and carries a lower risk of introducing contaminant microbes that might have colonized a commercial natto package after production.
Industrially, nattokinase is produced using wild-type Bacillus subtilis natto strains. Different strains produce significantly different enzyme yields. In one study comparing strains, the same soybean substrate yielded 88 FU/g with one strain and 347 FU/g with another. You won’t typically have strain-level control at home, but using a reputable spore powder from a natto supplier gives you a reasonable starting point. These are available from Japanese food suppliers and some online fermentation retailers.
Using Beans Other Than Soybeans
Soybeans produce the highest nattokinase activity of any legume tested, but they aren’t your only option. Research comparing European-grown legumes found that chickpeas and red lentils both produced measurable fibrinolytic activity when fermented with Bacillus subtilis natto, with activity estimated in the range of 7 to 350 FU/g depending on the strain used. Green peas and lupins also fermented successfully, and in several nutritional categories (vitamin K2 content, free amino acid content, and aromatic compound diversity) they actually outperformed soybeans.
Brown beans were the one legume tested that showed no fibrinolytic activity at all. If you’re avoiding soy due to allergies or preference, chickpeas and red lentils are the most promising alternatives, though you should expect lower nattokinase output than soy.
Why Home Production Has Limits
The nattokinase in homemade natto is real and biologically active, but extracting and concentrating it into something resembling a supplement is not a home kitchen project. Industrial nattokinase production involves separating the enzyme from the fermentation broth, then purifying it through techniques like three-phase partitioning (which uses ammonium sulfate and an organic solvent to selectively precipitate the enzyme at specific pH and temperature conditions) or multi-step chromatography. These processes require lab equipment and chemical reagents.
The enzyme is also sensitive to heat. Wild-type nattokinase begins losing activity as temperatures climb well above body temperature, with engineered variants showing melting points around 73 to 77°C. This means cooking natto after fermentation, or adding it to very hot food, will destroy the enzyme. If your goal is to consume nattokinase, eat the natto at room temperature or only slightly warmed.
Keeping Your Fermentation Safe
The core safety principle is simple: sterilize everything before inoculation, and maintain fermentation temperature consistently. Holding the beans at 40°C favors Bacillus subtilis natto over most pathogens, but only if you start with a clean environment. Specifically:
- Sterilize containers and utensils in a 120°C oven before use.
- Work fast after the beans are cooked. The window between cooking and inoculation is when contamination is most likely.
- Don’t open the fermenter during the 18 to 24 hour incubation. Each opening introduces outside air and drops the temperature.
- Discard batches that smell strongly of ammonia, have unusual colors (pink, green, or black spots), or lack the characteristic sticky threads.
Bacillus subtilis itself has a long safety record in food production and is generally recognized as safe. The risk comes from other organisms that might colonize the beans if given the opportunity, which proper sterilization and temperature control effectively prevent.