Second fermentation explained: from flavouring to carbonation

Second fermentation is where fermented drinks become truly your own.

It is the stage where flavour develops, carbonation forms and kombucha or kefir transforms from a simple fermented drink into something unique.

While many fermenters combine flavouring and carbonation into a single step, others prefer separating them into distinct phases for greater control over flavour and fizz. Both approaches work well — the choice depends on your goals and brewing style.

What is second fermentation?

Second fermentation begins after primary fermentation is complete and the main culture has been removed.

For kombucha, this means removing the SCOBY.

For kefir, this means straining out the kefir grains.

At this stage, the remaining microorganisms continue fermenting available sugars. This process develops flavour and produces the carbon dioxide responsible for natural carbonation.

It is also the perfect time to add fruits, herbs, flowers, spices, juices or syrups.

For most fermented drinks, second fermentation has two main goals:

developing flavour
building carbonation

More about benefits of second fermentation:

Benefits and flavours of the second fermentation

Flavouring and carbonation: together or separate phases?

Traditionally, flavouring and carbonation happen simultaneously during second fermentation. Fruits, herbs or other flavourings are added directly into a bottle, where flavours develop while carbonation builds at the same time.

This method is simple, effective and widely used.

However, some fermenters prefer dividing second fermentation into two separate phases. The drink is first flavoured and infused with fruits or herbs, then strained and bottled for carbonation.

You may occasionally see the carbonation stage referred to as a third fermentation. In reality, fermentation never truly stops between these steps, so many consider both phases part of the same second fermentation process. The term “third fermentation” is simply a convenient way to describe the final carbonation stage after flavouring ingredients have been removed.

Benefits of separating the phases

After experimenting with both methods, we found that separating flavouring and carbonation often provides more control over the final result.

Some advantages include:

cleaner flavour profiles
less sediment in the bottle
easier bottling
more predictable carbonation
no fruit pieces trapped in narrow-neck bottles
reduced risk of over-extracted herbs or overripe fruit flavours

The downside is that the process takes slightly longer because flavour extraction and carbonation happen in separate steps.

Stages of second fermentation

Stage 1: Flavour development

The first stage focuses entirely on flavour extraction.

Fruit, herbs, spices, flowers, juices or syrups are added to the fermented drink and allowed to infuse for one or two days.

During this time they release:

flavour
aroma
colour
natural sugars

This stage allows endless flavour combinations while preserving the character of kombucha or kefir.

It can also help balance acidity. Sweeter fruits and syrups can soften overly tart kombucha and create a smoother flavour profile.

For flavouring phase we love to use second fermentation bottle that is airtight and glass with wide-mouth, because of the easy cleaning and also carbonation build up.

Flavour ideas for kombucha:

Kombucha flavour ideas we tried and our hints for second fermentation

Flavour ideas for water kefir:

Water Kefir Ideas for Recipes that will quench Your Thirst

Flavour milk kefir:

Plain Milk Kefir taste not for you? Flavour it!

Stage 2: Straining and bottling

Once the desired flavour has been achieved, the drink is strained and all flavouring ingredients are removed.

At this point:

flavour extraction is complete
sugars have dissolved into the liquid
fruits, herbs and spices are no longer needed

The filtered liquid is then transferred into airtight bottles.

Stage 3: Carbonation

Once bottled, the cultures continue consuming available sugars and naturally produce carbon dioxide.

Because fermentation now takes place inside a sealed bottle, the gas becomes trapped in the liquid and creates natural carbonation.

In general:

more sugar = more carbonation
more time = more carbonation
warmer temperatures = faster carbonation

The result is a clean, naturally sparkling fermented drink.

Whether you choose to combine flavouring and carbonation or separate them into individual phases, both methods can produce excellent kombucha and kefir. We simply found that dividing the process gives us cleaner bottles, better flavour control and more consistent carbonation.