Natto tastes (and smells) the way it does because of a specific cocktail of volatile chemicals produced during fermentation. The bacterium used to make natto breaks down soybean proteins into ammonia, pungent acids, and earthy compounds called pyrazines, while simultaneously producing a sticky polymer that gives it a texture unlike almost any other food. If your palate rejects natto, it’s reacting to real chemical signals, some of which overlap with the smell of decay.
The Chemicals Behind the Smell
Natto is made by fermenting cooked soybeans with a bacterium called Bacillus subtilis. This microbe produces powerful protein-digesting enzymes that tear soybean proteins apart into free amino acids. That process releases ammonia as a byproduct, which is the sharp, almost cleaning-product-like note you notice the moment you open a container of natto.
But ammonia is only part of the picture. As those free amino acids break down further, they become precursors for a range of volatile organic compounds. The most prominent are pyrazines, a family of molecules that smell earthy, roasted, and musty. Specifically, 2,5-dimethylpyrazine and 2-methoxy-3-methylpyrazine are among the signature aroma compounds. On their own at low levels, pyrazines can smell pleasantly nutty (they’re found in roasted coffee and chocolate), but in natto they show up alongside ammonia and 2-methylbutanoic acid, a short-chain fatty acid with a sweaty, rancid quality. The combination is what makes the smell so polarizing.
There’s also 2,3-butanedione (the same compound that gives movie-theater popcorn its buttery smell) and 2-pentylfuran, which has a beany, slightly metallic quality. Individually, some of these compounds are perfectly pleasant. Together, in the concentrations natto produces, they create a layered aroma that many people’s brains interpret as a warning sign: something has gone off.
Why Natto Gets Worse With Age
If you’ve noticed that some natto smells worse than others, you’re not imagining it. The fermentation itself diversifies the aroma profile, but the real intensification happens during post-ripening, the period after fermentation when the product sits and continues to develop. During this stage, pyrazine concentrations increase significantly. Esters (fruity-smelling compounds) also rise, which is why very ripe natto can smell simultaneously funky and oddly sweet. The longer natto sits in your fridge past its ideal date, the more ammonia accumulates and the stronger the smell becomes.
The Texture Problem
For many people, the taste is secondary. The real barrier is the texture. Natto is famously slimy and stringy, producing long, gooey threads when you lift it with chopsticks. This comes from polyglutamic acid, a polymer that the bacteria produce during fermentation. Polyglutamic acid is a chain of glutamic acid molecules linked together, and it forms the sticky, mucus-like coating that clings to the beans and stretches between them.
This texture has no real equivalent in Western cuisine. Humans tend to associate sliminess with spoilage or with things that shouldn’t be eaten, so the mouthfeel triggers a visceral rejection in people who didn’t grow up eating it. Stirring natto before eating actually increases the stickiness, which is the traditional preparation method in Japan but can make the experience even more challenging for newcomers.
It’s Actually Full of Umami
Here’s the paradox: the same fermentation process that creates all those off-putting aromas also loads natto with glutamate, the amino acid responsible for savory, umami flavor. Fermented natto contains roughly 9.5 grams of glutamate per 100 grams, a concentration that rivals aged parmesan cheese. If you can get past the smell and texture, the actual taste on your tongue is deeply savory and complex, not unlike a strong aged cheese or miso paste.
This is why people who love natto genuinely love it. The flavor itself is rich and satisfying. The problem is that your nose processes information before your taste buds do, and for many people the aroma shuts down the experience before the umami ever registers.
Even Japan Is Divided on Natto
It’s worth knowing that natto isn’t universally beloved even in Japan. Consumption is highest in eastern Japan, where natto has deep cultural roots, but significantly lower in the Kansai region (Osaka, Kyoto) and the western part of Honshu. Researchers attribute this to a “food-related cultural inhibition,” meaning that natto simply wasn’t part of the food tradition in those areas, and people raised without it are much less likely to enjoy it as adults.
A study published in the Journal of Physiological Anthropology examined which characteristic of natto most affected people’s preferences and found that smell was the biggest factor. People who disliked natto pointed to the odor first, appearance second, and taste third. This lines up with what food scientists know about acquired tastes: repeated early exposure is what builds tolerance, and without it, the brain’s default response to pungent fermented foods is rejection.
Ways to Make It More Tolerable
If you want the nutritional benefits of natto but struggle with the sensory experience, a few approaches can help. The traditional Japanese method is to add karashi (hot mustard) and soy sauce, which cut through the ammonia smell and add familiar flavors that your brain can latch onto. Chopped green onion is another common addition that masks some of the funk. Kimchi, which has its own strong fermented flavor, can also redirect your palate.
Temperature matters too. Cold natto straight from the fridge has a milder smell than natto at room temperature, because fewer volatile compounds evaporate into the air when it’s chilled. Fresher natto (closer to its production date) will also be less pungent, since the pyrazines and ammonia haven’t had as much time to accumulate during post-ripening.
Some people find success by mixing natto into other dishes rather than eating it straight: stirred into hot rice (which absorbs some of the slime), folded into an omelet, or blended into a stir-fry where other strong flavors dominate. The goal is to dilute the texture and aroma while still getting what natto offers nutritionally.
Why People Push Through the Taste
Natto is the most concentrated natural source of vitamin K2 in the MK-7 form, which plays a key role in bone health and calcium regulation. A single 50-gram serving (about one standard package) provides roughly 380 micrograms of MK-7, a dose that clinical studies have linked to improved bone density markers. Natto also contains nattokinase, an enzyme with strong clot-dissolving properties. Research has shown it can break down nearly 90% of blood clots in a lab setting within six hours at therapeutic concentrations, and human studies have found measurable effects on blood clotting markers after a single oral dose.
None of that makes the taste better, but it explains why natto has a devoted following despite being one of the most divisive foods on the planet. For many regular natto eaters, the flavor eventually shifts from repulsive to neutral to genuinely enjoyable, following the same arc as other strong fermented foods like blue cheese, durian, or surströmming. The biology of the food doesn’t change. Your brain’s interpretation of it does.