Probiotic foods and drinks — Photo: Keisuke Tanigawa

Photo: Keisuke Tanigawa

The best Japanese probiotic food and drinks to try in Tokyo

These items not only help support improved gut health, but also facilitate better sleep, blood pressure, weight loss and more

Wednesday 1 April 2026

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Written by Christopher House

Associate Editor, Time Out Tokyo

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If you're the type to reach for vitamin drinks for their purported health benefits, this one might be for you. When it comes to gut healthy probiotic foods, you might already know about kimchi or kefir, but do you know your natto from your narezushi? Your koji from your katsuobushi?

Pretty much all of these items can be found in your local grocery store, or in some cases the nearest convenience store or even vending machine. Hunt around and see which ones you like – your gut just might thank you.

Note: the information in this article is for general informational purposes only and is not intended to serve as medical advice.

RECOMMENDED: Got a sweet tooth? Try these dessert omakase

To eat

Natto

Photo: Keisuke Tanigawa

Starting off strong we have the ever-divisive natto. Traditionally, this dish was made by soaking and steaming soybeans, then stuffing them into bundles of rice straw, a natural carrier of the bacteria necessary for the fermentation process.

Nowadays, most manufacturers skip the rice straw and spray the soybeans with bacteria directly, but the end result is the same after fermentation is complete: a pungent, sticky mass of beans with a distinct flavour and slimy texture. An acquired taste to be sure, but the Japanese delicacy is jam-packed with nutrients and beneficial bacteria.

Try eating natto on white rice with a splash of soy sauce and mustard plus a bit of green onion. For the extra adventurous, crack a raw egg on top, mix it all together and enjoy. Around ¥129

Umeboshi (pickled plum)

Photo: Keisuke Tanigawa

Lip-puckeringly sour with a salty sweetness, pickled plums are a fundamental part of Japanese culinary history. Foot soldiers used them during the Warring States period (1467–1568) to help with battle fatigue, while samurai mixed them into rations for an energy boost centuries later. Though you might not be fighting any battles anytime soon, perhaps a pickled plum or two will help you power through your work day.

There are many ways to eat umeboshi, but the simplest is to plop one onto a bowl of plain rice or stuff it into an onigiri (rice ball). For Western dishes, try adding a plum to your next bowl of muesli, oatmeal or salad for an extra pop of flavour, but mind the pit. Around ¥399

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Nukazuke

Photo: Keisuke Tanigawa

Nukazuke is just one kind of Japan's many types of tsukemono (pickled veg) – other traditional Japanese pickling methods include using sake lees, miso, soy sauce, vinegar and more. The term nukazuke refers to foods that have been pickled in rice bran. Dishes pickled this way have a nutty, tangy flavour that's a bit sour but not unpleasantly so, and are said to aid in digestion.

If you find the version with the bran still on to be a bit off-putting, try nukazuke that's had the powder washed off; you get the probiotic benefits either way. If you'd like to make your own, we taught you how to make nukazuke during lockdown, so head to the kitchen and start pickling again like it's 2020. Around ¥239

Miso

Photo: Keisuke Tanigawa

What's not to love about miso? This versatile paste made from fermented soybeans comes in many varieties and is used for everything from soups to salad dressings in both Japanese and international cuisine alike.

From white to yellow to red miso, the darker the paste, the longer the beans have been fermented. White miso paste is creamy, a bit sweet and good for lighter dishes, while yellow and red miso pastes are more concentrated with a richer, more umami taste.

Regardless of the type you use, you're still getting those probiotic benefits, so go nuts (or should we say go beans?). Around ¥813

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Soy sauce

Photo: Keisuke Tanigawa

This condiment needs no introduction. It may come as a surprise that soy sauce can be a probiotic food; it's simply a matter of finding the right kind. Most commercial soy sauces undergo a pasteurisation process, which ultimately destroys their probiotic properties.

The kind you're looking for will have the symbol 生 (nama, or 'raw') on the front. Find it in premium stores like Matsuya Ginza (head to B2) or Meidi-Ya. ¥1,150

Koji

Photo: Keisuke Tanigawa

Koji isn't a food typically eaten on its own, but rather a type of mould that's used to aid in the fermentation of other foods.

It's an absolute superstar in the world of Japanese cuisine, as koji is responsible for the production of the aforementioned soy sauce and miso, plus sake, mirin and more. Koji was officially declared Japan's national fungus in 2006, so it's kind of a big deal.

If you want to take a deep dive into Japanese cuisine and try making your own condiments and the like from scratch, chances are you'll need to get your hands on some koji sooner or later. Around ¥338

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Katsuobushi (bonito flakes)

Photo: Keisuke Tanigawa

These tasty morsels are used to garnish all manner of Japanese dishes from okonomiyaki (savoury pancakes) to hiyayakko (silken tofu), and are also an important ingredient in the cooking stock known as dashi.

They're made from skipjack tuna that has undergone a highly involved fermentation process that can last anywhere from a few weeks to several years, depending on the quality of the flakes.

Just like with soy sauce, make sure to get the right kind of bonito flakes for the probiotic benefits – the ones you want are called 'honkarebushi' (本枯節). ¥920

Narezushi

Photo: Keisuke Tanigawa

If you're a fan of anchovies, narezushi may be your cup of tea. It's the precursor to modern-day sushi and has an extremely salty fish taste. Narezushi is an umbrella term, as there are several kinds of narezushi throughout the country, with each region utilising its own type of fish and fermentation methods.

Pictured above is funazushi, a form of narezushi hailing from Shiga prefecture and made from crucian carp. Find it at speciality stores like Cocoshiga near Nihonbashi Station. Pair it with a nice sake or white wine and try it with a bit of soy sauce, wasabi and ginger. PS, eat only the fish slices, not the rice. ¥1,944

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Yoghurt

Photo: Keisuke Tanigawa

Though yoghurt isn't strictly a Japanese invention, the country offers a seemingly endless variety of the stuff. The six products featured above come from food company Meiji, each with their own strain of 'good' bacteria for a specific purpose: A1c yoghurt for blood sugar management, PA-3 yoghurt to control uric acid levels, LG21 yoghurt for stomach issues and so on.

The pink one is for skincare, while the R-1 and the Bulgarian-style 'Home Made Story' yoghurts are both for overall gut health. Try experimenting to see which one works best for you. From ¥149

To drink

Amazake

Photo: Keisuke Tanigawa

Remember how koji mould is used in lots of traditional Japanese cuisine? Here's another example. Amazake is a fermented rice drink that can be enjoyed hot in the winter or cold in the summer. Probiotics aside, the sweet, non-alcoholic beverage is known as 'drinkable IV' for its many additional nutritional benefits. (There's a version made with sake lees that contains a tiny bit of alcohol, but less than 1%.)

If you really want to dive deep into the world of amazake, check out our detailed guide on where to find the nutrient-rich refreshment around Tokyo and how to make it at home. From ¥189

Yakult

Photo: Keisuke Tanigawa

Ah, Yakult. The quintessential Japanese yoghurt drink dates all the way back to the 1930s. Invented by the late microbiologist Dr Minoru Shirota, what is now known as a tasty little health drink was once intended as preventative medicine against gut-related infectious diseases like cholera and dysentery.

The unique strain of L paracasei bacteria Dr Shirota created 90 years ago is still used in Yakult today, though we dare say cholera and dysentery aren't nearly as big of an issue in Japan as they used to be. Still, a Yakult a day certainly doesn't hurt. From ¥150

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My Flora Free

Photo: Keisuke Tanigawa

While Yakult's been around for decades, this one's a newbie. Released only in August 2025, My Flora Free is the creation of dairy company Nomura Dairy Products. Despite the 130-year-old company's name and usual specialisation, this particular product is totally plant-based.

My Flora Free is Japan's first certified low-FODMAP probiotic beverage, making it a good choice for those with sensitive stomachs. The bacteria it contains is the same found in sauerkraut and kimchi, so if you don't like those foods but still want their benefits, drink up. You can find it at your nearest Natural Lawson. ¥259

iMuse Immune Care

Photo: Keisuke Tanigawa

Kirin is probably best known for its beer, but it's got its hand in the food and healthcare industry as well. The company launched its line of iMuse immune care products in 2020, winning Product of the Year the following year for its health benefits.

The refreshing beverage comes in five different flavours, each inundated with 100 billion L lactis Plasma bacteria, a strain meant to aid in protection against viral infections like the flu and common cold. ¥120

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Kirin Oishi Immune Care

Photo: Keisuke Tanigawa

iMuse isn't the only probiotic beverage from Kirin. The company's 'Delicious Immune Care' probiotic beverage is relatively new, having been launched in 2023. Like its predecessor this yoghurt drink also contains the L lactis Plasma bacteria, but the key difference lies in the taste.

The OG iMuse drink is admittedly a bit watery, since its main function upon invention was to deliver its health benefits and not much else. The new-and-improved Delicious Immune Care drink on the other hand is, well, delicious. It delivers the same good bacteria as iMuse, but with a tastier, creamier yoghurt flavour. ¥140

'Plus Calpis' probiotic drinks

Photo: Keisuke Tanigawa

Like Calpis? This duo might be to your liking. Though Calpis is called a 'cultured milk beverage', the drink doesn't claim to offer any gut-healthy probiotic benefits (though its lactic acid does help aid with digestion). That's where these babies come in.

These drinks offer the goodness of Calpis plus the probiotics. The blue one contains an L gasseri strain meant to aid with sleep, while the red one claims to boost immunity and relieve allergy symptoms. ¥120

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Gun Gun Gurt

Photo: Keisuke Tanigawa

Here's another from Asahi: Gun Gun Gurt. The eccentric name is a mix of the Japanese word gungun, which more or less means 'steadily', plus yoghurt. Steady yoghurt? Sign us up.

This sweet, Yakult-like drink combines the benefits of the red and blue duo above, claiming to improve both gut health and sleep quality at the same time. Steady indeed. ¥190

Kaneka's Q10 yoghurt

Photo: Keisuke Tanigawa

This pretty pink bottle comes courtesy of health and wellness company Kaneka Your Health Care. The company specialises in various supplements from energy powders to its 'Moist Well' capsules, intended to help those who struggle with dry mouth.

While we can't speak to how moist this yoghurt drink will keep your mouth, it's certainly tasty. It includes coenzyme Q10, a powerful antioxidant with a wealth of health benefits ranging from improved cardiovascular health to migraine reduction. The main selling point of this drink, though, is its ability to help with fatigue, sleep quality and stress reduction. ¥139

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Megumi's gasseri yoghurt

Photo: Keisuke Tanigawa

Probiotic drinks aren't just about stronger immunity and better sleep. This beverage by Megumi contains a strain of L gasseri that's meant not only to improve gut health, but also to reduce body fat. There's an edible variation that comes in a cup, plus a capsule form too, for those who don't like the taste of yoghurt. ¥162

'The one with MBP'

Photo: Keisuke Tanigawa

This yoghurt drink – also by Megumi – contains MBP (milk basic protein), a compound that increases bone mineral density. The recommended dose of MBP is 40mg daily, which is precisely how much the drink contains – just make sure to drink it consistently to get the benefits.

It's a good choice for the elderly, women in general or anyone concerned about bone health and longevity. ¥118

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Morinaga yogurt drinks

Photo: Keisuke Tanigawa

Morinaga is well-known for its sweets (Hi-Chew anyone?), but it's got its hands in many baskets, including manufacturing dairy products. Pictured above are just two of the company's many yoghurt varieties.

The one on the left utilises the bacteria strain BB536 to help alleviate symptoms of IBS and improve overall gut health, while the bottle on the right contains MKP, a compound that helps manage blood pressure and blood sugar. ¥155

Bifix

Photo: Keisuke Tanigawa

Last but not least we have this Bifix beverage, part of a yoghurt line developed by Glico. While the Osaka-based food company's more popular products like Pocky and Pretz have likely added to more than a few waistlines, this beverage of theirs is meant for those looking to lower their BMI.

The drink is supposed to help enhance your resting energy consumption, ultimately leading to reduced body fat. So, if you scarf down a box of Pocky, then knock back one of these, do they cancel each other out? Only one way to find out. ¥139