how to make nattō in an instant pot

(Due to the popularity of our post on DIY homemade nattō, there have been requests for us to share detailed instructions on how we make nattō in our Instant Pot.)

diy homemade natto - how to make natto in an instant pot

Instant Pot Nattō

Holly White -
Healthy, homemade nattō, made using an Instant Pot.
5 from 1 vote
Prep Time 14 hrs
Cook Time 1 d
Total Time 1 d 14 hrs
Course Side Dish
Cuisine Japanese
Servings 12





  • Rinse and drain two cups of soybeans and place in a large mixing bowl.    
  • Fill the bowl with water, covering the beans by about an inch (3 parts water : 1 part beans).
  • Cover with a clean cloth or dish towel to keep out dust and soak overnight (approximately 12 to 18 hours).
  • Drain the beans and rinse with fresh water, removing any broken or bad beans.


  • Transfer the beans from the steamer basket into the Instant Pot stainless pot and add enough water to completely cover the beans (about 1 inch above the beans).
  • Set the pressure vent to “seal” and cook the beans on “Manual” for 20 minutes. Allow the pressure to come down naturally for 10 minutes.


  • While the soy beans cook, bring a few cups of water to boil in a small pot or tea kettle.  You'll use this water to sanitize your tools.
  • Lay out anything that will come in contact with the beans on a cooling rack over the sink (large mixing bowl, mixing spoon, thermometer, small glass dish, etc.). 
  • Slowly pour boiling water over everything to quickly sanitize.
    Note: Keep about two teaspoons of hot sterilizing water to activate the nattō cultures in the next step.
  • Note: I have always had great results with this method, however, if you feel more comfortable fully sterilizing your tools, place them in boiling water for at least 5 minutes.

Preparing the Beans

  • After 10 min. of natural pressure release, open the pressure release valve on the Instant Pot. (I recommend covering it with a cloth to keep the hot water from splashing). 
  • Using your sterile mixing spoon, remove one soybean to test for doneness.  It should be soft in the center and able to be smashed between your fingers with gentle pressure. If it's too mushy, the beans are overdone and will not be usable for nattō.
  • Place the stainless IP steamer basket into the sink or over a large pot.  Remove the beans from the IP and drain into the IP steamer basket.  Then pour the beans back into your large mixing bowl.
  • Place the steamer basket back into the Instant Pot.


  • Using the spoon that comes with the spores, add one spoonful of the nattō spores to the small glass dish.  Add about two teaspoons of remaining hot sterilizing water to the natto spores and mix with a sterile spoon.
  • Add the nattō starter culture mixture to the beans and stir gently but thoroughly to evenly distribute the natto culture. 
  • Dump the beans back into the steamer basket inside the Instant Pot.


  • Cover the pot with sterilized cheesecloth (or dishtowel) and then cover the pot with the glass IP lid. This will keep the beans moist, but prevent condensation from dropping on the beans.
  • Set the Instant Pot to the yogurt setting ("YOGT") for 24 hours. The temperature should remain between 90 and 104 F (30 - 40 C). Even though the Instant Pot does a good job of maintaining the temperature, I like to keep the thermometer in the pot and check it every so often.
  • The beans may take anywhere from 22-24 hours to ferment. When they are complete, you will see a fine white "fuzz" and stringy strands covering the beans. To test, you can gently stir a small area of beans. If gooey strands form easily, the natto is finished.
  • Natto has a distinct, pungent smell. What you don't want is a strong ammonia odor.  This means the beans have been over fermented and won't taste good.


  • Once the cycle is finished, let the beans cool for about an hour, then place the beans in the refrigerator to “age” for one to three days. This will slow down fermentation and enhance the flavor.
    diy homemade natto
  • To prepare the natto, add the desired amount of natto to a rice or cereal bowl and mix vigorously with a spoon or chopsticks.  Add soy sauce and finely chopped green onions to taste.  Serve over hot rice, warm mochi, or simply topped with diced toasted nori for a Paleo version.


We usually put the nattō in two separate containers before aging so that once complete, we can keep one in the fridge to eat within the week and then store the other in the freezer for later.
Also, if you notice your nattō is not very sticky, you may need to get a fresh batch of spores.  Good luck and enjoy!
Keyword ferment, instant pot, natto, soybeans
how to make nattō in an instant pot

As you read and try out our recipe please keep in mind this is a work in progress.  We are still experimenting and trying new tweaks.  Please share your findings in the comments below to help us all in the never-ending quest to make that perfect batch of delicious homemade nattō!


  • 5 stars
    testing review feature…

    • Which yoghurt setting. Nobody says. There’s two. One is low one medium the high is boil pasteurize. Somehow nobody is mentioning which one to use

      • I set my ip to custom and 104 degrees ( the lowest it would go). If you don’t have custom, I’d recommend the low setting because the instructions indicate a temperature of approximately 100 degrees.

  • AWesome! Thank you.

  • Excellent, this was my first attempt at making natto and it worked! I mixed these instructions with others that I found online and I now have a nice batch of natto aging in my fridge. I used store bought natto instead of natto spores. It was a tedious process but worth it!

    • Yes, the process can be a bit of work, Tina, but I agree with you…totally worth it! Congrats on your success! Glad you were able to “make it your own.” 🙂

  • Thank you for this and I will definitely try your recipe. One question- How do you sterilize a cheese cloth?

    • Hi Ume! You can sterilize the cheese cloth by simply pouring boiling water over it as in step 3 of the Sterilization step. Honestly, I have a hard time finding cheesecloth here in Puerto Rico, so I usually just use a few layers of dry paper towels instead. That may not be technically correct, but I’ve never had a problem and it works great. 😉

      • I use a silicon lid trimmed to fit inside the instapot instead of cheese cloth. I can sterilize it with the boiling water from the tea kettle.

        Also, are you supposed to seal the instapot or keep it on venting on the yogurt setting for the 24 hrs to do the natto? I am doing a batch and forgot to seal it.

        Thanks for the instructions!

        I am a puertorrican in CA.

        • Hi Didi. Great to hear that a fellow islander that is making natto at home! The silicone lid is an interesting idea, especially since you are able to sterilize it. Are you saying you use that to catch the water that drips from the IP lid during fermentation? My only concern would is that it may prevent oxygen from reaching your culture, which I think could lead to a weaker fermentation and less stringy natto when finished… That said, I’ve read that some people tightly seal the beans while they ferment and still get great tasting natto! How did yours turn out?

          I use a glass lid for my Instant Pot, not the sealing lid that is used for pressure cooking. I do this for two reasons: 1) I like to be able to see the beans while fermenting, as well as the temperature via the thermometer that I keep in the pot during fermentation. 2) To allow oxygen to reach the beans.

  • I think I posted my question with a wrong email address so trying again – how do you sterlize a cheese cloth?

  • I don’t have a steamer insert and have been making the natto directly in the ss liner, works just fine too. After cooking the soybeans I drain, cool a bit, return to pot, and add starter, cover top with a paper towel then lid, and set on yogurt for 24 hours. I also learned in Korea they make something similar called Cheonggukjang using wild bacillis without the need to buy starter, but fermented almost twice as long, then ground into a paste. Curious to try it someday, sounds like it could make a great non dairy cheese like spread.

    • That’s great, veggietater! I’m glad the stainless insert alone worked for you; I’ll have to give it a try. When I first started making natto (in my pre-IP days), I had read that the beans needed to be quite shallow in the fermenting vessel to allow for maximum exposure to the starter culture (only 3 beans deep). However, with the IP, you run into an issue of space….the steamer basket was my answer to that limitation. Cheonggukjang does look interesting! I wonder if I inadvertently made it once when I had “over-fermented” my natto beans. The aroma and texture sound just like what I got…if only I had known, it was still edible! ;D

  • Where to you get the starter for the natto

    • Cultures for Health sells spores. You can buy natto and use as a starter if you have an Asian Grocery nearby. Amazon also sells spores.

  • Diane Brincaccio

    One question: When you return the cooked, inoculated beans back to the Instant Pot, do you need to have water below the steamer for the 24-hour “yogurt” setting?

  • Good question, Diane. I’ve made two batches and it doesn’t get stringy. The white spores are definitely there but I’m wondering if it’s more than bad starter. Would moisture help?

  • Excellent recipe. I have 8qt no lid and no strainer. 20 hours perfect for ferment time! Saran wrap towel for lid. So easy so fast awesome flavor.

  • Good recipe. I have an instant pot like cooker without a yogurt function so I use a separate yogurt maker set at 100 F for 24 hours. The sticky natto makes it really hard to wash the bowl used for eating so I use a disposable styrofoam bowl and just toss it after use (not enviromentally friendly but nobody is perfect). Note that ready made frozen natto in the store comes in a styrofoam package.

  • +frugal alert +
    I wonder if you have tried to reuse the batch you made as a starter for the next batch?

    • Great tip, Iboshi! Yes, I have used some natto from a previous batch as starter. I did this by freezing small portions (about 1/4 cup each) of my initial batch (don’t forget to label them). While the beans were steaming, I pulled out one portion of starter from the freezer to thaw, and then mixed it in to the cooked beans to inoculate. Similar to yogurt, I wonder if the potency of the starter might weaken over time, so I have only done this using a “first generation” batch of natto. Honestly, I have enough set aside at this point, I don’t know if I’ll need to test that theory any time soon. Additionally, the starter culture does have an expiration date, so I tend to use that first and reserve my frozen starters for an emergency backup.

    • I have used store bought as starter. I am freezing some from this batch just for that! Thanks for the tip!

  • Pingback: diy homemade nattō! (and yogurt) - At Home in Puerto Rico

  • I am in the process of my second batch of instant pot natto and it’s looking stringy and smelling funky 🙂 I used a piece of my last natto batch for starter and started my first batch with store-bought natto. I’ve done things a little differently:
    – I cook my soybeans straight in the pot. No issues with burning or anything sticking.
    – one big difference is that I use a bit more starter and really swirl it around. I used half a pack of store-bought (thawed) natto and stirred it around with my cooked soybeans very thoroughly – there was already some stringiness from stirring it around before incubating. This made for super stringy natto when I was finally done.
    Thanks so much for your guidance!

    • Wonderful Lulu! Thank you for sharing your success.😀 I am anxiously awaiting an order of soybeans so I can test out making the natto directly in the steel pot. Now is the perfect time to get extra nutrient dense foods in our diet. Cheers!

  • yumiko nelson

    I don’t have a yoghurt setting on my IP. Should I set it on the warm setting?

  • You want to use the medium setting as it is approximately 100 F. The lower setting is ideal for tempeh at 95 F.

  • We do our natto very similar but still a bit differently. I steam my natto beans, which I purchase from laurasoybeans, in a steamer basket (3rd party) specifically made for my IP. They are pressure steamed for one hour with NPR. When I remove the lid, the beans have changed to a lovely, honey gold color, which is what we want. Then I allow them to cool for about twenty minutes, transfer the beans from my steamer basket directly into the metal insert pan in my instant pot, innoculate with frozen natto sport, add a few tb of water or bean juice from the steaming, close the lid and I use the middle yogurt setting. The lower setting is ideal for vegan yogurt, or tempeh, but not for natto. Natto requires more heat, so the middle yogurt temp is ideal for natto. This most recent time I ran my IP for 36 hours, which is the longest I’ve ever ran it, and I got the best batch of natto ever. It had the right smell, stronger strands, no ammonia smell, and was virtually perfect. Now it’s maturing in my fridge for a week, but I suspect it will be as good as it smells.

    And what I like, in particular about this method is the elimation of plastic. Virtually all plastic, especially plastic wrap, has a synthetic form of estrogen, and this makes its way into our bloodstream via our food and drink. Want to know what all this nasty plastic is doing to us, as a species? Look up a film called The Disappearing Male, which is an indie film made by a Canadian citizen. It’s shocking to see the decline of the male population is directly linked to plastic.

    Actually, I’ll link it here. Happy Natto making. Oh, and for the record, natto, tofu, and tempeh, all contain plant estrogen called phytoestrogen that has no effect on our estrogen levels. So any anti soy folks will use the “estrogen in soy” to scare you way. When, in fact, all animal products including dairy milk, goat milk, cheese, meat, contain mammal estrogen known as IGF-1.

  • Simply rinsing things with boiling water is not sterilising. In order to sterilise with water, items needs to be fully submerged and boiled continuously for at least 5 minutes on a rapid boil at 100°C. Then they’ll be properly sterilised. Basic school science 😉

    Natto contains a large amount of vitamin K2, which is essential for keeping calcium in your bones rather than too much going to the arteries and joints.

    • Great point Shaz! While not technically sterilization, I have used this method to quick sanitize my tools for years and have had wonderful success. That said, we have updated the post to include steps for sterilization by boiling.

  • Quick and easy black bean natto:

    I prefer black beans to avoid estrogen found in soybeans.

    I tried using two cans of Costco organic black beans (less than a dollar per can), rinsed well, and spread 1/2 inch thick in a stainless bowl with natto culture and covered with plastic wrap.

    Instant pot was set to yogurt with a bit of water in the bottom of the pot and covered with a large upside down glass oversized lid.. I left for 22 hours but I think it could use more than 24 because it’s not as stringy as regular natto.

    I aged it in the fridge for a few days and it tastes great! …much like black bean natto I’ve made in the past.

    I mix it with a mustard sauce I make from Dijon mustard, toasted sesame oil, maple syrup and a lot of garlic powder. Super tasty to my buds!

    Thanks for the tips on instant pot natto!


    • Thanks for the suggestion and recipe Ken 🙂 We’ll definitely have to give black bean natto a try! I have heard nearly any type of bean will work, and using black black beans also increases the protein content (win-win!).

      A quick note on estrogen and soy. While soy contains some phytoestrogens, the research seems to be somewhat inconclusive that it has a negative affect on the body. While it does have potential to cause negative side effects for men, the risk seems to be more associated with high intake and baseline heath. Additionally, there have been several studies that show it has a protective effect for women entering menopause as well as for certain types of cancer (including breast cancer). Whichever type of natto you make, the nutritional and immune benefits are undeniable!

      • Holly, what you’ve said is simply untrue. Asians have been eating soy for hundreds, if not thousands of years. Soy doesn’t have estrogen and the phytoestrogen in soy whether fermented, or not, is quite beneficial. Anyone claiming anything to the contrary, probably works for Weston Price, or is on their payroll as they are the organization that launched an all out attack of lies about soy. There is nothing inconclusive about soy. Phytoestrogens simply do not act the same as mammalian estrogen. “The quantity of phytoestrogen found in one cup of cooked soybeans can potentially decrease the risk of breast cancer by 25%”. This was a quote by Dr. Michael, Greger, M.D.

        Also, the main form of mammalian form of estrogen, called estradiol, is 100 times more dangerous than phytoestrogen. Of course, you probably know nothing about this since all you are doing is regurgitating information put out by Weston Price that has spread across the www like a virus. Please look up Colleen Patrick Goudreau’s two part video called It’s Just A Bean. It’s available on youtube.


        Actually, here you go.

        Part 1
        Part 2

    • Ken, Weston Price has created a lot of scare around soybeans that is simply not true. There is no estrogen in soy. There is phytoestrogen, which is plant estrogen. It does not raise our estrogen levels. In fact, the only place where you will find an abundance of animal or mammalian estrogen is in the food that you are already eating if you eat meat. Mammalian estrogen is found in cows milk, goat milk, cheese, meat, pork, etc. Oh, and butter too since it is made from milk. You also get a great doses of IGF-1, which is not something that any human needs. And for the record, black soybeans also have phytoestrogen. So if you really want to avoid estrogen, go plant based. Otherwise you’ve probably exceeded your dose for the day by consuming eggs, bacon, dairy milk, etc.

    • Ken, would you share your mustard sauce recipe? I’m new to natto and trying everything to make it more palatable for me.

      • I can’t give an exact recipe, but I can list the ingredients in order of my estimate of quantity. Dijon mustard (the large majority), toasted sesame oil, maple syrup, rice vinegar, tamari, roasted garlic powder, black pepper. Sometimes I use Umeboshi vinegar to replace some of the salty/sour taste. You could add rooster brand sriracha sauce or anything else you think might be good. Mix in a bowl, tasting as you go. Have an empty glass salad dressing bottle ready to fill, and save the rest for refills in the empty mustard jar. Keep in the fridge and add to natto or anything else where it seems like it might be a good idea. I also use it as part of a bread crumb dipping mix with a beaten egg for baked (thawed, frozen) salmon fillets in a toaster oven around 350 degrees F for ten minutes plus maybe a minute or two at 450.

        • For the baked salmon, the last couple minutes should be using the broil function indyrad of bake, hoping for a bit crispier result. Please correct me if you find a better temperature program.

  • I use about 2 cups of water under my 3rd party basket from amazon. I pressure steam for one hour and then NPR.

  • So sorry I missed this message. Since the beans have soaked, I add around two cups of water. If you have a 6 quart you can probably get away with 1 to 1 1/2 cups.

  • Can you fact-check a claim that using Natto as a starter reduces the amount of K2 in the batch? I’m frustrated that starter needs to be ordered from Japan and shipping cost is more than the product.

  • I just finished the high pressure 30 minute session. At about 8 min into it, the steam was shooting out. After 3 min of steam shooting, I sealed the pressure. When it beeped later on, I got a bath towel, used a fan over the top, and released the rest of the steam. I tested and the beans were the perfect texture. My setting was simply “high” -NOW it is sitting for 24 hours in a fermenter at 32 degrees C….My test is this: After it cooled, I dumped the liquid and using a santitized spoon scooped the beans into my fermenting pot (MLGB brand)….then I took a container of Natto from the fridge (overnight thaw), and scooped half the package into the beans with no liquid, just the moisture around them, and I stirred thoroughly, till it seemed all was sticky, then I took a custom cut piece of boiled and cooled cheese cloth and placed it over the beans with my hand which may not have been sterile. In 24 hours, I will follow your plan- cool 1 hr, then scoop into sanitized serving savers, continue fermenting in fridge 1-2-3 days and then freeze

  • For the IP owners: you can steam sterilize stuff in the IP, at sea level is 10′ pressure cook set on high.

  • @Eli – you don’t need to pasteurize or boil the already pressure cooked beans. Also, any boiling will kill any live culture. So no, do not use the boil setting.

  • I’m using two 6 1/2 inch Pyrex square bowls on top of the trivet in an eight quart IP. Insert a chopstick or shish kabob stick to separate. Two 6 1/4 inch round Pyrex will also fit. Each bowl can hold the cooked equivalent of two scant cups of dry soy beans. I’m so greedy use over two cups dry beans each bowl. Each bowl is covered with plastic wrap punctured with many holes from a tooth pick. Hot IP water left after lifting out the cooked beans in a stainless steel mesh bowl is poured onto the empty bowls stacked in the sink, separated by the wood stick, to sterilize the two bean dishes plus the spoon and bowl for thawed commercial natto additive. Before the hot water is poured i have the beans cooled off after 20 minutes in the mesh bowl, digging a crater in the full bowl of beans to aid the cooling process, tossing once after the first 10 minutes.

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