Homemade Japanese Miso from Scratch: Traditional, Gut-Friendly, and Easier Than You May Think

CONTENTS

• About This Recipe

• Recipe Overview

• Nutrition and Gut Health Benefits

• Ingredients

• Instructions

• Important Notes & Traditional Tips for Making Miso

• Final Thoughts

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ABOUT THIS RECIPE |

In Japan, making miso at home used to be completely normal — especially in winter. Families would gather, mash soybeans by hand, and let time do the work.

This recipe follows natural fermentation (天然醸造) — no shortcuts, no artificial heating, no artificial flavor and preservatives. Just natural ingredients, microbes, and patience.

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RECIPE OVERVIEW |

• Prep Time: 24 hours (soaking)

• Cook Time: 1–1.5 hours

• Total Time: 6+ months fermentation

• Equipment Needed: Pot or pressure cooker, large bowl, container, weight

• Difficulty Level: Medium

• Suitable For: Gluten-free, dairy-free, vegan

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NUTRITION & GUT HEALTH BENEFITS |

• Natural probiotics from fermentation

• Supports gut microbiome diversity

• Soy isoflavones for antioxidant support

• Enzyme-rich koji enhances digestion and umami

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INGREDIENTS |

• 600g dried Organic yellow soybeans (≈1.5kg cooked)

• 350g natural sea salt

• 1.2kg dried rice koji (fresh koji if available)

• 350ml soybean cooking liquid

• 20g sea salt (for surface)

• Sake spray (about ½ Tbsp sake)

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INSTRUCTIONS |

A traditional, natural fermentation method (天然醸造)

Step 1: Soak the Soybeans (24 Hours)

1. Rinse the dried soybeans thoroughly under running water.

2. Place them in a large bowl and cover with 3–4 times their volume in water. The beans will expand much more than you expect, so give them space.

3. Let them soak for about 24 hours at room temperature.

4. The next day, you’ll notice they’ve nearly doubled in size (in the picture). This slow rehydration prepares them for even cooking and smooth fermentation later.

Step 2: Cook Until Finger-Soft

Discard the soaking water and transfer the beans to a pot with about 2.5 liters of fresh filtered water.

You can cook them in two ways:

• Pressure cooker: About 20 minutes once pressurized

• Regular pot: Bring to a boil, then reduce to a gentle simmer for 1–1.5 hours

The most important test is texture. The beans should mash effortlessly between your fingers or with your chopsticks. If they resist, continue cooking. Proper softness ensures a smoother paste and more even fermentation.

Step 3: Save the Cooking Liquid (Don’t Waste It)

Drain the cooked soybeans — but do not discard the cooking liquid.

This broth contains valuable water-soluble nutrients like isoflavones and saponins, along with a naturally gentle sweetness. It’s both functional and delicious.

Reserve about 350ml for the miso mixture.

I personally use the rest in miso soup. Nothing is wasted.

Step 4: Mix Rice Koji and Salt First

In a separate large bowl, combine:

• Rice Koji

• Natural sea salt

Break up any clumps and mix thoroughly.

Step 5: Mash While Warm

Allow the soybeans to cool until they are warm but comfortable to touch.

Mash them into a paste using your hands (traditionally), a masher, or a food processor.

Making miso by hand is not only traditional — it’s personal. The natural microorganisms on your hands participate in fermentation, contributing to what we call “my-kin” — your own household microbial signature.

NOTE: Small bits are okay. Perfect smoothness is not necessary.

Step 6: Combine Everything Thoroughly

1. Add the salt-koji mixture to the mashed soybeans.

2. Using your hands, mix carefully and evenly until fully incorporated.

This is where transformation begins. Make sure there are no streaks of unmixed soybean paste. Uniform mixing ensures safe and balanced fermentation.

Step 7: Adjust to “Earlobe Softness”

1. Gradually add the reserved soybean cooking liquid.

2. Mix thoroughly between additions.

You’re aiming for the texture of your earlobe — soft, pliable, slightly springy, but not loose.

This traditional texture test ensures proper moisture for long-term fermentation.

Step 8: Form Balls & Remove Air

1. Take a handful of the mixture and form a tight ball in your hands, pressing firmly to push out trapped air.

2. Place it into a sterilized container and press down strongly to eliminate gaps.

3. Repeat until all the miso is packed tightly.

Air is the enemy here. Mold thrives on oxygen, so compress thoroughly.

Step 9: Protect the Surface

Pressing the soybean mixture to smooth the surface

Spraying sake on the surface

Sprinkling sea salt across the top

Once fully packed:

1. Smooth the surface flat

2. Lightly spray with sake

3. Sprinkle 20g of sea salt evenly across the top

The salt and alcohol act as natural mold deterrents.

Step 10: Cover and Add Weight

Cover the surface with plastic wrap

Placing a flat lid

Placing 1kg of stones

Sealing the container with a lid

1. Cover the surface tightly with plastic wrap, ensuring the miso is not exposed to air.

2. Place a flat plate or lid directly on top.

3. Add approximately 1kg of weight.

4. Seal the container with a lid.

The weight helps:

• Release trapped air

• Allow tamari-like liquid to rise and form a protective layer

• Encourage even fermentation throughoutrrents.

Step 11: Let Time Do the Work (6+ Months)

Store in a cool, dark place away from direct sunlight.

Traditionally in Japan, miso is prepared in winter. The cold temperature suppresses unwanted bacteria and allows fermentation to begin slowly and safely.

Step 12: Check Occasionally

Over time, a dark tamari-like liquid may form on top. This is normal and flavorful. If you notice surface mold, remove it generously along with surrounding miso. Then continue fermenting.

I’ll also be sharing the fermentation progress over the coming months on Instagram @kojiandmore if you’d like to follow along!

Patience is part of the recipe...

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IMPORTANT NOTES & TRADITIONAL TIPS FOR MAKING MISO|

• Sterilize Your Container

  Always sanitize your storage container with boiling water (or proper sterilization) before use to reduce unwanted bacteria.

• Making Miso by Hand (“My Bacteria”)

  Traditionally, miso is made with bare hands. The natural microorganisms on your hands participate in fermentation and create a unique household flavor, often called “my-kin” (my bacteria).

  
  

  The relatively high salt concentration (about 12–13%) suppresses harmful bacteria, allowing fermentation to proceed safely. However, make sure you have no cuts on your hands. Wash thoroughly before starting, and wear gloves if needed.

• Remove Air Thoroughly

  Mold thrives on oxygen. Press the miso firmly into the container, eliminate air pockets, cover tightly, and use a weight. Minimizing air exposure prevents mold growth and oxidation while supporting safe fermentation.

• Use Weight

  The weight gradually compresses the miso, releasing air pockets and allowing natural tamari liquid to rise to the surface, creating a protective barrier. This supports safe, balanced fermentation over time.

• Proper Storage During Fermentation

  Store in a cool, well-ventilated place away from direct sunlight. If using glass containers, be especially mindful of light and temperature fluctuations.

• Don’t Waste the Soybean Cooking Liquid

  The cooking liquid contains valuable water-soluble nutrients, including isoflavones (antioxidant support) and saponins (which may help regulate cholesterol and blood sugar levels). It also has a gentle natural sweetness — use it in soups or drink it instead of discarding it.

• Best Season to Prepare Miso

  Miso is traditionally made in winter because colder temperatures reduce unwanted bacterial growth and allow fermentation to begin slowly and safely. According to miso professionals, the ideal schedule is to prepare miso between January and late May and begin enjoying it after October, once it has matured fully.

• Natural Fermentation (天然醸造)

  Homemade miso ferments naturally at room temperature rather than through industrial heat-controlled methods. It follows the rhythm of the seasons — slow in winter, more active in summer, and mellowing in autumn — developing deeper umami and complexity over time. Fermentation speed will vary depending on your local climate.

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FINAL THOUGHTS |

Homemade miso is more than food — it’s time, tradition, and your own microbial story.

Once you try it, store-bought miso will never taste the same 🥢✨

Follow us at @Kojiandmore on Instagram for any updates and progress!