You prepare your kombucha carefully, lift the fabric of the jar… and there’s a surprise. Brown filaments, suspended particles, a thick deposit at the bottom. At first sight, this might seem dirty, even worrying. Many beginners immediately think. « my kombucha is contaminated », « it’s not clean », or « I’ll get sick if I drink this ».

In fact, most of these deposits are simply a sign that your kombucha is… alive. By definition, a fermented beverage is not a perfectly homogenous, transparent liquid. It’s normal for yeast, bacteria and tea residues to leave visible traces.

The aim of this article is to help you distinguish between :

• normal deposits and filaments, typical of healthy kombucha
• warning signs
• cases where it’s really time to throw things away and start afresh with a clean culture

We’ll also look at how you can adapt your habits to limit visual surprises, while keeping your drink effective, aromatic and pleasant to drink.

Reminder, what’s really going on in your jar

To understand what you’re seeing, you first need to remember what kombucha is.

A living ecosystem, not just a drink

A jar of kombucha contains :

• a SCOBY, a gelatinous disc of cellulose in which bacteria and yeast live
• an acidified starting liquid, rich in micro-organisms
• a sweet tea that serves as food for this small community

Yeasts consume the sugar and produce alcohol and CO₂. Bacteria transform the alcohol into organic acids and build the cellulose matrix that forms the SCOBY. This permanent work leaves traces in the form of :

• yeast residues
• SCOBY micro-fragments
• cellulose filaments in formation
• tea pigments

So it’s logical that homemade kombucha should be livelier and more textured than a perfectly filtered industrial drink.

Why are deposits particularly visible in homemade kombucha?

Industrial kombuchas are often :

• finely filtered
• sometimes pasteurised
• standardised to meet the expectations of consumers used to clear drinks

At home, you work with a live culture and a glass jar. Everything that happens in the fermentation remains visible. It’s sometimes confusing, but that’s also what makes the experience interesting.

If you use a quality strain, for example a well-balanced live SCOBY and its starter liquid supplied by a specialist producer, at least you know that what you’re seeing comes from yeasts and bacteria adapted to kombucha, not unknown micro-organisms.

Normal deposits and filaments in kombucha

Before talking about contamination, let’s take a look at what is normally found in a healthy jar.

Brown filaments attached to the SCOBY

The famous « brown filaments » are one of the most common scenes. They can be seen :

• hanging under the SCOBY like little roots
• floating in the liquid
• sometimes gently settling to the bottom

These are generally :

• clumps of dead or excess yeast
• fermentation residues linked to yeast activity
• sometimes a mixture of yeast and cellulose in formation

These filaments can be :

• brown, dark beige or almost black
• soft, gelatinous, slightly elastic
• smooth (not fluffy or dry)

This is all normal. You can filter them when bottling if their appearance bothers you, but they are not dangerous in themselves.

The deposit at the bottom of the jar

As the days go by, the yeasts multiply and then some of them die or detach. They then fall to the bottom of the jar, forming a deposit of varying thickness.

This deposit :

• is often brown or dark beige
• may be compact or slightly muddy
• thickens with each batch

Again, this is not a sign of trouble. Many kombucha brewers even choose to remove some of this deposit from time to time, to rebalance the culture, but a certain amount of yeast at the bottom is perfectly normal.

Suspended particles

You can also see :

• small pieces of SCOBY that have come loose
• fragments of cellulose in formation
• tea residues (especially if the leaves have not been finely filtered)

These suspended particles sometimes give the drink a slightly cloudy appearance, rather like homemade cider. This does not mean that the drink is ‘dirty’, but that it is poorly or not at all filtered.

The gelatinous veil that forms on the surface

During fermentation, a thin gelatinous layer forms on the surface of the liquid. This is the beginning of a new SCOBY. This veil can :

• appear as a translucent film
• trapped bubbles
• have thicker and thinner zones

This is not mould, but a cellulose matrix produced by bacteria. Over time, it thickens and becomes a new disc.

3. How can you distinguish normal deposits from a real problem?

The big question is. How do you know if what you’re seeing is healthy or worrying?

To do this, you can use three main criteria:

• texture
• the colour
• position (surface or depth)

Texture, gelatinous or downy?

In general :

• what is gelatinous, viscous, stringy or smooth to the touch comes from yeast, bacteria or cellulose. This is typical of normal fermentation.
• anything fluffy, dry, powdery or granular on the surface is more likely to suggest mould.

If you see a stain that looks like something growing on forgotten bread or stale jam, with the appearance of « dust » or a little hairy carpet, the alarm is more serious.

Colour, brown/beige or bright green/blue/black?

Normal yeasts and deposits are generally :

• beige
• brown (light to dark)
• sometimes almost black for older deposits

Worrying stains are often :

• green
• blue
• dark grey or deep black, but in the form of a dry, non-gelatinous spot
• very clean white, very dry, in small downy circles

The nuance is important. A SCOBY can have darker, mottled or brown-stained areas without this being a problem.

Position, above or below ground?

Mould needs oxygen. So they grow :

• always on the surface
• never deep in the liquid

The deposits at the bottom, the filaments hanging from the bottom of the SCOBY and the particles suspended in the kombucha are almost never mould.

If you see fluffy spots on the surface of the liquid, particularly if they are round, well-defined and green, blue or white in colour, it is probably mould.

Typical cases, normal or not?

To make things more concrete, here are a few typical situations.

have brown filaments coming down from the SCOBY

It’s practically the ‘postcard’ of homemade kombucha. In the vast majority of cases :

• it’s normal
• clusters of yeast
• this indicates that fermentation is going well

You can either :

• leave and strain just before serving
• or filter before the second fermentation in the bottle, if their appearance disturbs you visually

There’s a kind of brown mud at the bottom

This « mud » is nothing to worry about. It corresponds to :

• dead yeast
• tea and cellulose residues

If the jar has been left unstirred for a long time, it is normal for everything to accumulate at the bottom. You can :

• discard some of this deposit when cleaning the jar
• or leave it if the crop is stable and you like the taste

Small white pieces floating in the kombucha

These are often :

• mini fragments of new SCOBY in formation, which are detached
• small sheets of cellulose that move around in the liquid

They may surprise you when you see them in the glass, but they are not dangerous. If you prefer a cleaner look, filter when bottling.

have a green or blue patch on the surface, like down

This time, the scenario is very different. A spot :

• on the surface
• very clear green, blue, grey or white
• downy, dull, like a stain on mouldy bread

… is almost always mould.

In this case, don’t hesitate. Throw away the SCOBY and the liquid, and clean the jar thoroughly before starting a new crop.

What should be done with normal deposits and filaments?

Once you’ve been reassured that your deposits are ‘healthy’, there are a number of options available to you to make the drink more enjoyable.

Filtering when bottling

The simplest solution:

• pour the kombucha through a fine sieve (or a clean cloth filter)
• separating the beverage from the most visible filaments and deposits

You can :

• save the SCOBY and some of the liquid for the next batch
• dispose of the rest of the deposits in the compost or in the bin

This filtration stage does not affect the quality of the kombucha; it only removes the most visible solid elements.

Shake lightly before serving (as appropriate)

Some people prefer :

• leave a little sediment, particularly yeast sediment, for a very « lively » drink
• shake the bottle lightly before serving to homogenise the contents

But be careful:

• if the bottle is very fizzy, it’s best not to shake it too much to avoid causing it to overflow
• if you don’t like the deposit, it’s better to leave it at the bottom and pour gently

Accepting a visually imperfect craft drink

Part of the work involved in making homemade kombucha consists of :

• accept that not everything is clear-cut
• understand that the presence of visible yeast and bacteria is normal
• appreciate the artisanal, lively and spontaneous side of the drink

If you feel the need for a perfectly clear kombucha, you can of course filter more finely, but bear in mind that each additional filtration step takes away some of that raw character.

When deposits and filaments should alert you

Although most deposits are normal, there are situations where the appearance of the kombucha should give you pause for thought.

Simultaneous presence of deposits and suspect odours

If, in addition to the filaments, you notice that :

• kombucha smells of mould, damp cellars, rotten eggs, meat or chemicals
• the smell repels you immediately

… so don’t rely on filaments alone. Smell is a very important indicator.

In this case, it’s best not to consume the drink, even if you don’t see any clear patches of mould on the surface.

Very strange surface deposits

Certain deposits may be cause for concern if :

• they float on the surface in the form of small dry islands
• they have a granular appearance, like dust or sand
• they form well-defined circles or fluffy patches

If you are unsure, observe the surface for one or two days:

• if the « stain » spreads, becomes denser, and gains in relief and colour, it is probably mould
• if it dissolves, sinks or remains gelatinous, it is yeast or cellulose.

When in doubt, it’s best to err on the side of caution and throw everything away.

Abnormally coloured deposits

Very bright or unusual colours (fluorescent green, bright orange, intense pink) can also be a warning sign, particularly if they appear in small, well-separated patches.

Some infusions or fruit used in secondary fermentation can colour the drink, but in this case you know what you’ve added. If not, beware.

How can I limit the appearance of visually intrusive deposits?

If you have trouble with the ‘living’ aspect of kombucha, a few good practices can reduce the amount of visible deposits without harming the fermentation process.

Filter the tea well

Before adding the SCOBY and starter fluid :

• filter the tea to ensure that no leaves or tea dust are left behind
• use a fine sieve or paper filter

This avoids adding particles from the start that will later grow with the yeast.

Balancing yeast

Too much yeast can result in lots of filaments and a huge deposit at the bottom. To rebalance :

• from time to time, remove some of the yeast deposit from the bottom of the jar
• don’t systematically leave all the deposits from one batch to the next
• make sure the temperature is not too high, which would encourage a yeast explosion

A good quality, well-balanced SCOBY naturally has a more harmonious relationship between yeast and bacteria, which limits these excesses.

Don’t leave batches lying around for too long

The longer a batch is left to ferment, the more :

• the yeasts have time to work and then die
• the deposit increases
• kombucha gets closer to vinegar

If you like a rather mild drink, stop the fermentation in time and make regular batches, you’ll generally have fewer impressive deposits than in a jar you’ve forgotten about for two months.

8. Practical checklist when you see filaments or deposits

To gain confidence, you can follow this little checklist every time a jar seems strange to you.

1. I look at the surface of the kombucha.
   Do I see fluffy, dry, coloured spots (green, blue, black, very clear white) or simply a gelatinous, smooth, beige or translucent film?
2. I’m looking at the SCOBY.
   Is it supple, gelatinous, beige to brown, or is it dry, blackened and brittle?
3. I look at the bottom of the jar.
   Is it a brown « sludge » of yeast, or strange stains rising to the surface?
4. I smell kombucha.
   Vinegar, cider, yeast smell (normal) or musty, rotten egg, rubbish, chemical smell (problematic)?
5. If the smell is right, I taste a teaspoon.
   If the taste is consistent (sweet, sour, vinegary but clean), the deposits are probably normal.
6. I decide: filter or bin.
   If everything looks normal, I filter it and keep it. If any of the warning signs are present (mould, disgusting smell), I throw everything out.

With practice, these steps will become almost a reflex, and the presence of filaments will no longer cause you to panic.

Frequently asked questions, deposits, filaments and kombucha

Can yeast filaments be drunk?

Technically, yes. Yeast filaments and fragments of SCOBY are not toxic in themselves, and some people eat them without any problem. It’s mainly a question of mouthfeel.

If it disgusts you, filter it. If you don’t mind, you can leave them in.

Do the deposits mean that my kombucha is « stronger » or more probiotic?

Not necessarily. The amount of visible deposits does not directly reflect the total number of micro-organisms. Well-filtered kombucha can be just as rich in beneficial bacteria as very cloudy kombucha.

The presence of deposits mainly reflects the way you handle the wine (filtration or not), the length of fermentation and the yeast/bacteria balance.

Do I have to throw out the whole jar as soon as I see a brown filament?

No. A brown filament, especially if it’s under the SCOBY, is almost always normal. It’s the combination of « filament + coloured fluffy spot on the surface + bad smell » that should make you throw it out.

My kombucha is full of deposits but smells and tastes good, can I keep it?

Yes, if :

• pleasant smell (vinegar, apple, tea, sweet yeast)
• the taste is consistent (sweet, acidic, even very acidic, but clean)
• no visible mould on the surface

So the kombucha is edible. You can just strain it to make it look better.

How can you be sure that you’re starting with « good » deposits and not with lousy micro-organisms?

It all starts with the culture:

• a SCOBY of healthy live kombucha from a reliable source
• a sufficiently acidic starter liquid to protect the drink at the start
• clear instructions on the proportions of sugar, tea and fermentation times

By choosing a kombucha culture that has been tested, balanced and accompanied by its starting liquid, you know that the filaments and deposits come from yeasts and bacteria adapted to kombucha, not ‘wild’ micro-organisms.

Conclusion, deposits that reassure rather than worry

Seeing deposits or filaments in your kombucha is a bit like seeing the rind on a good cheese or the deposit in a natural wine. Surprising at first, but then you realise that it’s the sign of a living product, not a systematic defect.

Remember that :

• brown filaments, bottom deposits and suspended particles are generally normal
• the real warnings are downy mould on the surface and bad smells (musty, eggy, rubbish, chemical)
• you can filter as much as you like to make the drink visually « cleaner », without giving up fermentation

With practice, you’ll be able to tell at a glance what’s healthy and what’s not. And your deposits will no longer be a source of anxiety, but simply a visual stage in the life cycle of your homemade kombucha.