Natto pairs best with steamed white rice, which is by far its most traditional companion, but it also works surprisingly well with avocado toast, eggs, kimchi, and a range of toppings that can soften its strong flavor. Whether you’re a natto newcomer trying to make it palatable or a longtime fan looking for new ideas, the right pairing makes all the difference.
The Classic: Natto Over Rice
In Japan, natto over steamed white rice is the default. It’s a breakfast staple eaten daily by millions, and for good reason: the sticky, salty fermented soybeans draped over plain rice create a balance of flavor, texture, and nutrition that’s hard to improve on. The mild sweetness of the rice tempers natto’s funky bite, and the combination delivers protein, fiber, and complex carbs in one bowl.
To build a proper natto rice bowl, start by stirring the natto vigorously with a small amount of the included sauce packet or a splash of mentsuyu (a dashi-based sauce). Many people add a dab of Japanese mustard, which comes with most natto packs and cuts through the richness. Then spoon it over a bowl of warm rice and finish with chopped green onions, shredded nori, and soy sauce to taste. A raw egg yolk on top is another popular addition that makes the dish richer and creamier.
One note on raw eggs: the whites contain a protein called avidin that binds to biotin (a B vitamin) and reduces how much your body absorbs. The yolk doesn’t have this issue, so if you’re eating natto with egg regularly, using just the yolk or a soft-cooked egg sidesteps the problem entirely. Cooking the white denatures the avidin and frees up the biotin, so a poached or soft-boiled egg works perfectly too.
Pairings That Help With the Taste and Smell
Natto’s ammonia-like funk is the biggest barrier for newcomers. The good news is that several foods can mask or complement that intensity without dulling the experience. Kimchi is one of the most effective options. Its own pungent, tangy, garlicky flavor covers up the funkier notes of natto, and since both are fermented foods, they taste surprisingly natural together. Simply chop the kimchi and mix it directly into the stirred natto before serving over rice or eating on its own.
Other flavor neutralizers include pickled vegetables of any kind, fresh ginger (grated or minced), a squeeze of lemon juice, and a drizzle of rice vinegar. These acidic or sharp ingredients counteract the flat, musky quality that puts people off. Sriracha or chili oil adds heat and tanginess that similarly redirects your palate. If you’re just starting out with natto, loading it up with two or three of these strong flavors is a perfectly valid strategy while you develop a taste for it.
Modern Combinations Beyond Rice
Natto doesn’t have to stay in a Japanese flavor profile. Avocado toast with natto has become a popular fusion option, and it works because avocado’s creaminess and mild fat balance the sticky, sharp fermented beans. Spread ripe avocado on a thick slice of sourdough or multigrain toast, spoon stirred natto on top, and finish with nori strips and everything bagel seasoning for crunch. A splash of tamari or coconut aminos adds umami depth. Microgreens like radish or broccoli sprouts bring color and a peppery bite that complements the dish well.
Sourdough bread is a particularly good base because its own natural fermentation creates flavor complexity that matches natto’s intensity, and whole grain varieties add fiber and texture from seeds. Beyond toast, natto pairs well with brown rice, quinoa, savory oatmeal, and salad greens. It can be stirred into warm grain bowls, folded into omelets, or spooned onto crackers with a little cream cheese. The key principle is pairing natto with something that has either a neutral, starchy quality to absorb it or a bold enough flavor to stand up to it.
Why Fat Matters With Natto
Natto is one of the richest food sources of vitamin K2, specifically a form called MK-7 that supports bone density and cardiovascular health. But K2 is fat-soluble, meaning your body absorbs it much more efficiently when you eat it alongside dietary fat. A bowl of plain natto over white rice is relatively low in fat, so you’re not getting the full nutritional benefit.
Adding a fat source fixes this. Avocado provides heart-healthy monounsaturated fats. An egg yolk adds fat along with additional fat-soluble vitamins. A drizzle of sesame oil, a side of fatty fish, or even a few slices of cheese all improve K2 absorption. This isn’t a dramatic intervention, just a small habit that makes a meaningful difference if you eat natto regularly for its health benefits. A meta-analysis of Japanese studies found that habitual natto intake raises MK-7 blood levels and supports bone density, but the researchers specifically noted that fat co-ingestion optimizes absorption.
Gut Health Pairings
Natto contains Bacillus subtilis, a spore-forming probiotic bacterium that survives stomach acid and reaches the intestines intact. But probiotics do their best work when they have something to feed on, which is where prebiotic fiber comes in. Natto itself already contains oligosaccharides from the soybeans that increase levels of beneficial Bifidobacterium in the gut. During fermentation, the original soybean sugars transform into different oligosaccharides, but these still feed the same beneficial bacteria.
You can amplify this effect by pairing natto with other prebiotic-rich foods. Good options include garlic, onions (raw green onions do double duty as a flavor topping), leeks, asparagus, bananas, and whole grains like oats or barley. These foods provide additional fiber that supports the growth of Bifidobacterium, which in turn feeds other beneficial gut species through a process called cross-feeding. Essentially, the first wave of good bacteria breaks down fiber into compounds that a second wave of bacteria can use, creating a cascade of gut health benefits. Pairing natto with a fiber-rich meal rather than eating it in isolation gives those probiotics the best chance of making a lasting impact.
Quick Pairing Ideas
- Breakfast bowl: Steamed rice, natto, raw egg yolk, green onions, nori, soy sauce, and mustard.
- Avocado toast: Sourdough, avocado, natto, everything bagel seasoning, tamari, and microgreens.
- Kimchi natto: Chopped kimchi mixed into stirred natto, served over rice or eaten as a side.
- Grain bowl: Brown rice or quinoa, natto, pickled vegetables, sesame oil, grated ginger, and a soft-boiled egg.
- Savory oats: Steel-cut oats cooked with a pinch of salt, topped with natto, green onions, and a drizzle of chili oil.
- Simple snack: Natto on crackers with cream cheese and a squeeze of lemon.