Natto – Japanese Fermented Soy Beans

Last week it was nata, this week it’s natto.  Though both are delicious (and maybe a little challenging by some standards) they are not otherwise easy to confuse.  Nata is candy made from a kombucha, jun or vinegar SCOBY. Natto is an alkaline, Japanese, soy ferment that has had me smitten ever since I first read about its health benefits in (say it with me) The Art of Fermentation by Sandor Katz.

I had never tried natto before reading The Art of Fermentation, and after reading about it both there and elsewhere, I was intimidated.  Descriptors given both in my reading and conversation with Japan-dwelling friends: slimy, mucilaginous, disgusting, okay when you eat it with a ton of mustard, not for non-Japanese, bizarre, gross, funky, stinky and unpleasant.  That’s the short list. With those ringing recommendations,  it somehow kept getting pushed down in the rankings on the to-do list of my experiments. When I finally tried some in a restaurant and, later, others from the freezer section of my local Japanese market, I felt something between disappointment and confusion.  I was a little disappointed that natto wasn’t a bit more challenging and I was confused that everyone and their mother had described this food as slimy.

Soak your beans in an extra large vessel and cover them with at least twice as much water as there are beans.  They will more than double in size.

Soak your beans in an extra large vessel and cover them with at least twice as much water as there are beans. They will more than double in size.

Natto Texture

I hate slimy.  A lifetime battle with mushroom hatred and an inability to swallow certain items from certain regional foods has taught me that sliminess is my food dislike. Natto is not slimy.  If anything, it’s the opposite. Its changing web of strings and strands are on the sticky side. And I love them. My first through fifteenth bites of natto reminded me of a very toned down version of that time in the Peruvian rainforest when we snagged a few fruits from the latex tree.  As you might imagine, fruit from the latex tree has some interesting qualities, the main one being that your lips stick together for hours after you eat it, with no relief available from soap or water scrubs (the ambrosial flavor makes it worth eating anyway).  This is a way more exaggerated effect than the bit of cling you get from eating natto, but it was certainly a closer reference for me than anything mucilaginous that may have crossed my plate in the past.

Natto Taste

The flavor is a little bit roasty, a little bit funky (think blue cheese) and a lot soy.  For me, this is a wonderful thing.  Like many others, I gave up unfermented soy under duress.  I hit a pretty rough hormonal period (sorry, gents) and after an elimination diet, I learned that soy was the culprit for me.  As a long-time tofu lover, I was pretty distressed. But a crying-for-no-reason-fit in the middle of the street, and a few horrible bouts of cramps convinced me that the sacrifice was worth it.  Two years later, I’m my (arguably) sweet self all month long. But I do periodically get the strong desire to whip up a batch of super firm tofu and while natto doesn’t have a whole lot in common with tofu, the leguminous flavor does tame my soy-seeking beast.

Natto Spores

This spoon is so little. Teensy weensy spoon that makes it possible to get the right amount of nattomoto on your beans.

Natto Health Benefits

Natto is special for another reason: those health benefits I mentioned above. While most fermented foods become alkaline during the fermentation process due to increased mineral bioavailability, natto is actually just an alkaline food due to its key fermenting bacteria Bacillus Subtilis Natto. (More information on that in The Art of Fermentation by Sandor Katz, pg. 329). Better yet, an enzyme is produced during fermentation that is both clinically proven to do amazing tricks and suspected of having a few others up its sleeve. Most importantly, this enzyme, nattokinase, has been shown to do in plaques in the arteries and is suspected of having a similar effect on plaques in the brain (aka those bastards who cause all kinds of neurological disorders like the plague of alzheimer’s).  It is also used to tread tons of conditions, from heart disease and hemorrhoids to varicose veins and infertility. The many healthy properties are what had me sold, initially.  With a strong desire to avoid all aforementioned plaques, this miracle food sounded pretty good to me. Now that I eat it regularly, I dig it for the flavor.

Why Make Natto?

I make natto for the same reasons I make most things: it can be hard to find organic natto and I’m not a fan of GMO soy.  And, of course, homemade just tastes better.  Homemade natto is simultaneously funkier than commercial and definitely more intensely umami (think red meat or blue cheese). We’ve been using it all kinds of places that break with tradition, including seasoning with barbecue sauce and  making “natto pâté.”  The soybeans I use tend to be larger than the soybeans I’ve had in commercial and restaurant nattos, so if you were/are a regular consumer of commercially produced natto, do be prepared for that difference.


Natto’s so-called slimy texture is more like fun, sticky strings to me.


Although there is some equipment needed for this process, if you can make yogurt, you can make natto.  There are a couple things to consider, though: the amount of spore needed is TINY, so the quantity of beans you need to make is enormous (1 kilo of dried beans!).  You need to be able to maintain a warmer temperature (~103F) for 24 hours.  I do this with a heating pad with no off switch inside my oven. My experiments with culturing in jars did not go well, so I don’t think your typical yogurt maker is a good option here.

I bought my natto spores from Cultures for Health. The instructions included with the spores were good, but very focused on sterilizing everything in sight. I use my normal standards for fermenting when making natto, which for me means a very clean kitchen, clean implements, vessels and pots and no sterilizing.


  • shallow dishes sufficient to hold 1 kg of soybeans after they’re hydrated and cooked (I used my pyrex 4.8 quart baking dish, my 8-inch square pyrex dish and my
  • plastic wrap or aluminum foil (sadly, I’ve found that plastic wrap works best for natto in my home)
  • a large pot
  • a heating pad with no off switch or another device or process for maintaining a 104 degree temperature for 24 hours straight*
  • kitchen thermometer
  • a very large bowl, such as one you might use for sauerkraut production
  • a kitchen scale (optional)


  • 1 kilogram (2.2 lbs) dried, organic soy beans (seriously, buy organic, or you’re definitely getting GMO soy)
  • 0.1 grams natto starting spore (bacillus subtilis natto)


  1. Rinse soy beans and remove stones and unwanted beans
  2. Place beans in a large container and add at least twice as much water as there are beans
  3. Soak for 12 hours. Once the soaking period is over, drain the beans and place them in a very large pot.  Cover with water and bring to a low boil.  Allow to boil for 5-6 hours or until beans break apart easily but are not yet mush.
  4. Strain the beans. Allow them to cool slightly, for about 30 minutes.  While the beans are cooling, bring a 1/2 cup of water to a boil and allow it boil vigorously for 5 minutes.  Remove from heat and let it sit to cool for 10 minutes.
  5. Add your tiny, tiny spoonful of natto-moto spores to the water and stir vigorously until the spore powder is dissolved.
  6. Pour spore liquid over your cooked beans and stir very thoroughly to distribute the spores as evenly as possible.  I spend a good chunk of time stirring.
  7. Transfer inoculated beans to their culturing containers.  I use my pyrex baking dishes (think lasagna, not loaf).  You don’t want the sides very high and you don’t want the beans to be layered too deeply. 1-2 inches deep should do it. Cover containers with plastic wrap and place them on the heating pad in the oven, or use whatever contraption you use for incubation.*
  8. Wait 24 hours. Remove plastic wrap and stir beans.  You should see the characteristic natto strings.  The beans on the surface may look a tad cooked or wrinkled. It’s nothing to worry about.  Stir the beans to integrate the guys who were on the top. You can eat your natto after a couple hours in the fridge or store them in the fridge for a week.  I put half in the freezer as soon as it’s cooled. These quantities are not consumable by my family of two, and the freezer maintains their fun strands.

*There are many ways that one can do this.  If you do it my way, use a kitchen thermometer to measure the temperature of the various heat settings on your heating pad before you start this process. Keeping it between 100F and 110F has worked best for me.


  1. says

    Yesssss! I’ve been waiting for this post! I have fibromyalgia and have thought about taking a nattokinase supplement, but it’s really expensive and I’m more of a food-as-nutrition kind of gal. I actually give my cat a nattokinase supplement to reduce strain on his heart, at the advice of our holistic vet (he has a murmur). Natto here we come!

    • Amanda says

      That’s awesome, Priya! I’m so glad to hear it. I’d love to hear if you find it uber funky. I was honestly shocked at how not challenging it was when I first tasted it. To be fair, I eat ferments from around the world as a regular part of my diet, so maybe my weirdness tolerance is high. :-)

  2. says

    I like challenging and funky foods, so I am ready! Just gotta get the culture. Do you happen to know of any shops in Philly who sell the culture (preferably in smaller portions)? I’m going to be in Philly just about every weekend in May (vending at craft markets!), and it’d be awesome to avoid buying a crazy amount of culture and paying for shipping. :)

  3. Ann says

    This is one my my favorite foods. It took me 6-8 years of trying natto 1-2 times a year to develop a taste for it. Now I really do love it. The gooey,sticky, stringiness of it has never bothered me (I’m a good little Southern girl who loves her stewed okra), but the taste and smell is what took time for me to appreciate. My kids, on the other hand, have loved it almost from the start. All 3 of them, ages 2, 7, & 10, ask for it often. I think one factor to them wanting to like it was this video on youtube: .
    I have started making it myself using beans that are not soy. My most recent is with pintos. I just use part of a package of frozen natto as my starter. It turns out great. What I miss, though, is the seasoning packets. We usually shake a little fish sauce, soy sauce, and/or mustard on it.I think about slicing up a scallion to add in there, but my laziness takes over and I don’t actually do it.
    My advice for others who are first trying it – If at first you don’t like it, try, try, and try it again and again and again. You will eventually like it! (especially if you use the seasoning packets that come in the frozen natto!)

    • Amanda says

      Haha, Ann! Nice video.
      Did you get the strings with pintos? I tried a couple other kinds of beans that were definitely fermented, but not particularly stringy. It’s a deal breaker for me! I love the strings.

    • Drew says

      Oh this is great news for me! I live in Australia and I cannot find the spores anywhere, not even from Cultures for Health’s Australian affiliates. Disappointment! I will begin looking for frozen Natto asap, thanks!

      • Amanda says

        Hi Drew,

        You can definitely make natto without spores. It will take a bit longer to ferment, but bacillus subtilis is naturally present on the beans and is very heat tolerant, so cooking won’t kill it!

  4. Ann says

    They do have the strings. My heart and stomach did little happy excited flips when I stirred them up and saw the strings. Makes me laugh at how excited I get about it. They don’t get as foamy-stringy as regular natto when I do a big mix of them, but the strings are there. I have always used a package of natto for my starter, though. Maybe that makes the difference. I have never tried using just the spores themselves. If they didn’t get the strings I wouldn’t be as excited about them either. Hmm… That makes me a little bit hesitant to order spores. I’ve been contemplating ordering a package of natto spore and a bag of brown rice koji so I can make some non-soy miso. I’ll need to thinkbaout this, because if you, oh fermentation fab master that you are, don’t get strings with non-soy beans, I know I wouldn’t get them.
    Just read your most recent post. I am a very deep shade of green with envy that you have a restaurant you can go to that serves ferments. One of my cousins lives up there in Philly. I’m going to have to start talking to him more than once a year so that I can go visit up there with a free place to stay. You really make it sound like a wonderful place!

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  6. says

    Thanks for this blog Amanda and your enthusiasm for Natto. I would like to make it without adding natto spores and using non GMO soybeans. How long do you have to ferment the cooked beans without the spores? Can I put them into a jar in a closet or does it have to be in an oven? I have read that the heat should be a constant 100 degrees for fermentation. My oven does not go that low. I don’t want to use natto spores from Japan because of radiation.

    • Amanda says

      Hi Letha,

      The beans definitely need to be cultured in the range of 100 degrees (104 is ideal). They need to hold at that temperature for quite a while, and they need to be in a flat layer, so in a jar is definitely not a good idea.

      Some ideas for you: test the temperature of your slow cooker, test the temperature of your oven with the oven light on, fill a cooler with 104 degree water and check them frequently to make sure the temp has been maintained (add more hot water if not). There are lots of ways to get the right temperature, but it is an essential element for natto fermentation. The bacteria will simply not culture if the temperature is too high or too low.

      Good luck!

  7. Gloria says

    I am excited to find a recipe for making natto because after the radiation complication I have no longer bought it. HOWEVER: how can COOKED beans be fermented? I thought fermentation requires enzymes? Thanks for clarifying. Gloria

    • Amanda says

      Hi Gloria,

      A couple things: first, you’re inoculating with a spore in the recipe I’ve used here (although some do it without). Second, This is not lactofermentation. The bacterium responsible for natto fermentation is bacillus subtilis natto, and it is a strain of bacteria that tolerates temperatures way above what your average kraut-fermenting lactobacillus will.

      I hope that helps!



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