How to Bottle and Flavor Kombucha

2nd Fermentation

Now, for our favorite part: bottling and flavoring the kombucha! Bottling is an important part of the overall process and impacts the final taste of the brew. Here at Joshua Tree Kombucha, some of our favorite additions to our home brewed kombucha are passionfruit, lavender and dragon fruit. This next phase allows you to infuse your own creativity and favorite flavors into your kombucha.

Happy brewing!

How do I bottle kombucha?

Step 1. Remove and store your scoby

Remove the scoby from the 1 gallon jar and place in a clean container. Pour 1 to 1.5 cups of kombucha into the container with the scoby and cover with fermenting cloth. This will serve as your starter tea and culture for your next batch.

Step 2. Flavoring kombucha

If you are choosing to flavor your kombucha, add now to any airtight bottle or jar.  You can use your favorite combination of fruits (raw or frozen), herbs or juice.  Always be sure any flavoring is 100% natural with no additives.  You can create any blend you wish!

Visit to try some of our favorite recipes!

Step 3. Pour kombucha into airtight bottle or jar 

Using a funnel, pour your fermented kombucha into your airtight bottle or jar. Make sure to leave 1.5 inches of head space to avoid pressure build up.

Step 4. Seal and store bottles

Seal your bottles and leave at room temperature for 1-4 days. This will add carbonation to your kombucha.

Step 5. Check on your brew

Carefully open the tops of each bottle to allow C02 to escape every day. This will ease the pressure in the bottles and ensure the kombucha isn’t a fizzy mess when you are ready to drink it.

Have a teaspoon of the kombucha to see if the flavors have settled. If not strong enough, try again in a day.

Step 6. Refrigerate

Once optimal level of flavor and carbonation are reached, place bottles in the refrigerator to stop further fermentation.

Step 7. Enjoy your creation!

Drink up and share with friends! Don't forget to tag us on Instagram @joshuatreekombucha with all of your amazing creations.


how to bottle kombucha 
how to bottle kombucha

Bottling FAQ

Which bottles or jars should I use?

The types of bottles you choose for the 2nd fermentation can make or break your kombucha, literally. For anyone who has experienced a kombucha blow up, you know what we're talking about. The 2nd fermentation is all about building the carbonation and flavor in each bottle and that build up of co2 can be dangerous if not bottled correctly.

Here are some bottles we recommend using for this phase: 

EZ Cap (Flip Top) Glass Bottles:

If you like your kombucha extra fizzy and carbonated, this type of bottle is ideal. With airtight bottles, less co2 escapes and thus increases carbonation in the drink. The only time you loosen the cap a bit is to release some of the excess co2 build up each day. 

TIP: Always use round bottles as square and other shapes are more prone to explosions.

Glass Bottles with Screw-On Caps:

As long as the glass bottle is thick and the cap is made of strong steel, this method will work. Avoid using aluminum or plastic caps. The built up carbonation and level of acidity will deform these caps and can potentially cause them to pop off.

Stout Glass Bottles with Polyethylene Cone Caps:

An alternative to flip top bottles, these thick glass bottles use a threaded poly cone cap that allows the build up of co2. The caps will also curve slightly once the bottles are well-carbonated, providing an easy indicator for when your kombucha is ready to be refrigerated. 

How do I avoid a kombucha explosion?

One of the biggest culprits of bottle explosions is poor glass quality. To avoid this we recommend you never use vessels such as beer bottles, mason jars or thin glass such as Ikea flip top bottles. Having a strong, food-grade glass bottle with an airtight seal is very important for this phase. You can also store your filled bottles in an empty ice chest or bucket while left out at room temperature to allow for a safer, easier clean up in case of a bottle breaking.

How long do I leave the kombucha out during the bottling period (second fermentation)?

At room temperature (about 65-72°F), the kombucha should be out for at least 24 hours and no more than 4 days. After one day, try a teaspoon of the kombucha to see if the flavors have settled. If the flavors are not strong enough, try again in a day or two.

Note: Never shake the bottles! This will lead to a fizzy mess.

What flavors should I use?

Fresh fruits and herbs are recommended, especially when they are in season. If you want a healthy version of kombucha, lavender with lemon and honey is a great option. For a 16 oz. bottle, a good estimate is half a teaspoon of freshly squeezed lemon juice and half a teaspoon of raw honey with one teaspoon of dried lavender. Adjust flavoring based on preference. 

This is the fun part! Experiment with your favorite herbs and fruit to create your own favorite flavors.

For more recipes, check out the link here.

How much kombucha do I funnel into the bottle?

Funnel the kombucha into the bottle with 1.5 inches of head space. The less space you have, the more carbonation will form. 

How can you make your bottles “burp”?

Simply loosen the cap for a couple of seconds, let the air out and tighten the cap again. This lessens chances of excess build up causing an explosion. To be safe, have the bottles or jars stored in a cupboard or space where no one will be hurt if a bottle pops. 

Is "burping" completely necessary?

There are varying opinions on this but technically it is not necessary to release co2 from your bottle during the 2nd fermentation. Some experienced home brewers know exactly how many days to leave their bottle at room temperature for their preferred flavor/level of carbonation and will place the bottles into the refrigerator without opening. Once chilled, the kombucha becomes more bubbly and less fizzy when opened without sacrificing the co2 build up. Although this is a great technique for experienced brewers, for safety reasons we recommend releasing a small amount of co2 each day prior to refrigerating brew until you get the hang of whatever method works best for you.

How long does a kombucha brew last before it goes bad?

The longer the kombucha brews, the more acidic it will become. Good news: your kombucha will never “go bad." A longer brew just affects the taste of the kombucha as the fermentation process continues. You only have to worry once it strays from the flavor that you had in mind, but we recommend consuming within 3 weeks of refrigeration for best taste and quality.

How do I stop the 2nd fermentation?

Simply place the bottle in the refrigerator. The cold will slow the fermentation and prevent further co2 buildup.


  • We wouldn’t recommend corks for bottling as the pressure can eventually literally blow the top off. We recommend something more airtight like our swing top bottles.

  • Can you use bottles with corks such as wine bottles for bottling kombucha?


    Catherine kula

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