How to Clean and Sanitize your Fermentation Equipment

Are you a home brewer or fermenter enthusiast who wants to keep your equipment constantly clean, so you can successfully complete your projects?

You are right! Regularly cleaning and disinfecting your equipment ensures the quality of your fermentations and avoids the risk of contamination.

Whether you are preparing fermented vegetables, beer, kombucha, tempeh, or yogurt, it is in your best interest to clean and, sometimes, sanitize your equipment!

In this article, we provide you with all the information you need to effectively clean and sanitize your fermentation equipment. We explain what you need to do to keep your equipment hygienic:

  • the steps to follow,
  • the products to use,
  • the precautions to take.

Follow our advice to produce quality fermented food and avoid any risk of contamination in your kitchen!

Why Clean and Sanitize?

Because nobody wants to have an intrusive microbe spoil their fermentation!

Regular cleaning and disinfection of your brewing and fermentation equipment are essential to ensure the quality and safety of your preparations. Unwanted microorganisms can grow on equipment that is not cleaned and disinfected. This can affect the quality of your fermentations and even cause health risks.

It is also important to maintain a good level of hygiene to promote the growth of the desired microorganisms in your fermentations (lactic acid bacteria, yeast, koji…) and to avoid competition between your culture and unwanted microorganisms.

In some cases, a mere washing may be sufficient to eliminate potential contaminants, while in other cases, it is necessary to sterilize your equipment. This will prevent any risk of contamination and ensure the success of your fermentations.

There is nothing worse than beer or kombucha that smells like dishwashing liquid instead of hops and honey!


It is important to understand the differences between cleaning, sanitizing, and sterilizing to choose the right method for your fermentations.


Cleaning (synonymous with washing) means removing visible dirt with soap or detergent and water.

This step removes visible dust and dirt, but there will still be microorganisms on the surface or equipment.


Sanitizing (synonymous with disinfecting) means killing 99.9% of microorganisms on a surface or equipment. Food-grade sanitizers, such as Star San, are used to achieve this purpose.


Sterilizing means killing 100% of microorganisms and spores. Sterilization is not necessary for home brewing and fermentation!


When to Clean and When to Sanitize?

Each type of fermentation has different hygiene requirements.

Some fermentations are very vigorous and can resist contamination, while others can fail immediately if the fermentation equipment is not clean enough.

It is therefore essential to know the needs of your fermentation to choose the right cleaning and disinfection method.

However, it is important to note that sanitation cannot replace cleaning. Cleaning is always essential before starting any fermentation! So, remember to wash your hands and clean your equipment and work area before you start. This will minimize the risk of contamination and ensure the quality of the final product.

Special cases:

  • When you have moisture and mould problems in your home, it is crucial to thoroughly disinfect (sanitize) your fermentation equipment, regardless of the type of fermentation you wish to do.
  • If a fermentation has been contaminated with mould or kahm yeast, you will need to disinfect (sanitize) the contaminated containers, lids, and any other equipment.

Fermented Vegetables

  • Cleaning: required
  • Sanitation: optional

To prepare fermented vegetables, simply wash your jars and utensils with water and dish soap. This will remove visible dirt and minimize the risk of contamination.

There is no need to sanitize or sterilize your utensils for vegetable fermentations, as the lactic acid bacteria present on the vegetables create lactic acid, which eliminates all unwanted competition.

Beverages With Short Fermentation

  • Cleaning: required
  • Sanitation: optional

Fermented beverages that only require a few days of fermentation, such as kombucha, water kefir, tepache, ginger bug and sima are super easy to make at home and do not require sanitizing your equipment.

Wash jars and utensils thoroughly with hot water and soap before starting your recipes.

Fermented Milks

  • Cleaning: required
  • Sanitation: optional

Fermented milks such as yogurt, viili, matsoni, milk kefir and fresh cheeses do not require sanitation.

Wash jars and utensils thoroughly with hot water and soap before starting your recipe.

Most fermented milks create lactic acid during fermentation, which prevents contamination. Sanitation is therefore not necessary.

However, mature cheeses need sanitized equipment.

Moulds & Others (Koji, Miso, Tempeh, Natto…)

  • Cleaning: required
  • Sanitation: required

Fermentations of grains, cereals, and legumes from noble moulds, such as koji and tempeh, require cleaning and sanitation.
This is also true for fermentations such as miso and natto, which need competition-free conditions to develop properly.

Sanitizing gives your culture a head start, allowing it to eliminate the competition on its own.


  • Cleaning: required
  • Sanitation: required

Fermentations of alcohols such as beer, cider, wine, and mead require cleaning and sanitizing all equipment that will be in contact with the preparation of the beverage wort. This includes the carboy, airlock, lid, bottles, funnel, ladle, spoons, auto siphon, siphoning tube, etc.


How to Clean?

Cleaning consists of washing the equipment with soap and hot water. This is the first step before any sanitation of the fermentation equipment.

Steps for cleaning by hand:

  1. Wash your sink and rinse it.
  2. Fill with hot water and add dish soap.
  3. With a clean sponge, scrub the equipment to remove all traces of dirt.
  4. Rinse several times with cold water.
  5. Allow to air dry or dry with a clean cloth.

You can also wash the equipment in the dishwasher.

How to Clean Glass Bottles

Bottles, carboys, and tubes are always a challenge to clean thoroughly, as they have narrow necks, making it impossible to scrub by hand, or to wash effectively in the dishwasher. If left unchecked, residue will quickly build up on the inner sides.

There are two effective options for cleaning your bottles, carboys, and tubes: brush, or brewing soap.


A brush that fits the container you want to clean can work wonders. Add soap to your brush and scrub vigorously with a little water until it is clean as a whistle! Then give it a good rinse!

Brewery Wash

Brewery wash (PBW) is a specialized soap for dissolving organic residues. It’s super effective! It cleans carboys, glass bottles and tubes simply by soaking them.

Steps for using brewery wash:

  1. Rinse equipment to remove most of the dirt.
  2. Dilute 1 ½ tbsp. of brewery wash in 1 litre of warm water.
  3. Soak for a few hours.
  4. Drain and rinse well (4 to 5 times) to remove all traces of soap.


How to Sanitize?

Once your equipment is thoroughly cleaned, you can sanitize it by using a food grade sanitizer. This step will kill 99.9% of the microorganisms that are present.

It is essential to go through the cleaning step before sanitizing, as the sanitizer cannot dislodge and kill microorganisms embedded in dirt. Once your equipment has been cleaned, you will not need to scrub it when sanitizing.

This section will give you information on how to use the different sanitizers.

How to Use Star San

Star San is an acid-based liquid foaming sanitizer. It is biodegradable and kills harmful bacteria and mould.

  1. Dilute 1 tbsp. (15ml) in 10L of cold water.
  2. Apply with a cloth, sponge, vaporizer or by immersion.
  3. Leave in contact for 1 to 2 minutes.
  4. Allow to air dry.

The Star San does not need to be rinsed.

How to Use Io Star

The Io Star is an iodine-based liquid sanitizer. It is also called iodophor.

  1. Dilute 1 tbsp. (15ml) in 10L of cold water.
  2. Apply with a cloth, sponge, vaporizer or by immersion.
  3. Leave in contact for 1 to 2 minutes.
  4. Allow to air dry.

The Io Star does not need to be rinsed. However, over time it may stain plastic or vinyl. This will not affect their use.

How to Use Oxy-San

Oxy-San is a powdered oxygen-based cleaner and sanitizer. It does not contain sulphites, soap, or phosphates.

It can be applied to stainless steel, glass, and plastic.

  1. Dilute 1 tbsp. (15g) of Oxy-San in 1 gallon (3.8L) of hot water.
  2. Soak equipment for 2 minutes.
  3. Remove equipment and allow to air dry.

Oxy-San does not need to be rinsed. The residue even contains yeast nutrients!

How to Sanitize With Bleach

Bleach can be used to sanitize equipment, but it is not ideal. If not rinsed properly, bleach can cause fermentation to fail. It should only be used if you have no other options. Do not use bleach with plastic: bleach does not rinse well when in contact with plastic.

Use regular strength bleach with no distinctive odour.

  1. Dilute 1 tbsp. (15ml) of bleach in 10L of cold water.
  2. Soak the equipment for 5 minutes.
  3. Rinse thoroughly with hot water, at least 3 times.
  4. Allow to air dry.

Never mix bleach with other sanitizing products!


Other Sanitizing Techniques

Can I Use an Autoclave to Sanitize?

Yes, of course! An autoclave can even do more than just sanitize. Thanks to its high temperature and pressure, it can sterilize.

Can You Sanitize With a Dishwasher?

No. The average temperature of a dishwasher is around 55-60°C (130-140°F), which is insufficient for sanitizing.

Can I Sanitize With Rubbing Alcohol?

Yes, and no. It is not ideal!

Alcohol sold as a sanitizer in drugstores often contains bittering agents, which may end up in your food if not properly rinsed.

70% alcohol may be suitable for sanitizing surfaces, instruments, and hands (spray on and let dry). Be careful, contrary to what you might think, alcohol >70% is less effective than 70% because alcohol needs water to sanitize properly.

Can I Sanitize With Boiling Water?

Yes, and no. Scalding is not recommended because if not done properly, it can damage carboys and other glass equipment.

If you know what you are doing, then 15 minutes in boiling water will be enough to sanitize your equipment (but not your hands).

Can I Clean With Vinegar and Baking Soda?

No. Mixing vinegar and baking soda will not cause any physical damage, but it will not clean effectively either. This is due to their opposite pH levels: vinegar is acidic and baking soda is basic. When mixed, they neutralize each other, reducing their ability to clean. The result of their combination is mainly foam (CO2), water, acetate, and sodium ions.


Get Started!

Congratulations, your fermentation equipment is clean as a whistle! You can now start fermenting. For inspiration, here are some of our most popular fermentations:

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