When you start making kombucha, you know you’re handling a living culture… but you don’t always realise how sensitive it can be to its environment. All it takes is a badly rinsed jar, a dodgy tea towel, mouldy fruit or excessive heat for doubts to creep in: what if my strain of kombucha is contaminated? Can I save it, or do I have to throw it all away and start again from scratch?
This question is all the more stressful because you quickly become attached to your SCOBY. You feel you’ve invested time, tea, sugar and sometimes money to obtain a quality culture – for example a live strain bought from a specialist like Natural Probio – and the idea of having to throw it all away can be discouraging.
The good news is :
not all “anomalies” are real contamination;
we can often save the project, even if we sometimes have to give up saving the strain itself;
A few simple steps can then help you get back on a sound footing and prevent future problems.
In this long-format guide, we will go into detail, point by point:
what we really call a “contaminated” strain;
situations where it is imperative to throw everything away (without discussion) ;
cases where a rescue or at least a recovery test can be attempted;
how to clean, secure and restart ;
how to prevent your next jar from suffering the same fate.
1. What is a “contaminated” strain of kombucha?
We often use the word ‘contamination’ as soon as we see something a little odd in the jar. However, not every anomaly means that your kombucha is dangerous.
1.1 Real contamination vs. simple imbalance
There are two main cases:
Culture imbalance Fermentation works, but :
kombucha is too acidic, too sweet and too yeasty;
The SCOBY has a funny shape, but no fluffy spots;
there are a lot of deposits and brown filaments.
The strain is not ‘contaminated’ in the strict sense: it is alive, but poorly balanced. It can often be corrected (by adjusting fermentation time, temperature, hygiene, etc.) or ‘rejuvenated’.
Contamination by undesirable micro-organisms Here, other bacteria or fungi have taken over. This can be seen in :
Sinking SCOBY: not a sign of death or contamination; a new disc usually forms on the surface.
Beige, cream, light brown to dark brown: fermentation and tea gradually colour the SCOBY.
If you’ve already read the articles on “My kombucha is too acidic or too sweet, what should I do?” or “There are deposits or filaments in my kombucha: is this normal?”, you’ll know that these phenomena are not, in themselves, contamination in the strict sense.
2. Identifying genuine contamination: the signs that can’t be mistaken
To find out whether your strain really has a problem, you need to learn to spot the warning signs.
2.1. Mould on the surface: the clearest case
True mould typically appears as :
well-defined, island-shaped patches ;
at the surface of the liquid (never at depth);
dry or fluffy instead of gelatinous;
green, blue, dark grey, black or sometimes very clear white;
with a mouldy appearance on bread, cheese or jam.
This is the most important criterion: If you see such mould, the strain is considered contaminated in the strict sense.
In this case, the general rule is strict but simple: Throw everything away. No saving, no scraping, no “I’m keeping the underside of the SCOBY that looks healthy”.
2.2. Bad smells: when the nose says “no
Even if there’s no visible mould, the smell can be a sign of contamination.
It is normal for kombucha to smell:
vinegar (such as mild cider vinegar) ;
cider, green apples, white grapes ;
sometimes yeast or a slight smell of beer.
On the other hand, it’s no longer normal if you feel :
damp cellar mould, wet cardboard ;
rotten egg or gas ;
the rotten meat, the rubbish, the extreme cheese that grabs you by the throat;
solvents, household products and scented washing-up liquid.
These odours indicate that other micro-organisms, or chemicals, have invited themselves in. Even without coloured stains, this is a form of contamination.
small worms or larvae (which can happen if the jar is not properly protected).
Here again, the rule is clear: don’t collect the strain. An insect that has been lying around on dirty surfaces, rubbish bins or decomposing food can bring with it bacteria or fungi that have no business being in your drink.
3. Saving the stock… or saving the project?
The title of this article asks a deliberately ambiguous question: “How do you save a contaminated strain of kombucha? The first thing to accept is that you can’t always save the strain itself. On the other hand, you can save the kombucha project by starting again from a healthy base.
3.1. Situations where no attempt should be made to save the strain
Let’s be very clear: in these cases, we don’t try anything on the SCOBY, nor on the liquid.
Mould visible on the surface, however small.
Rotten egg, mould, dustbin or solvent smell, even without visible mould.
Presence of insects, larvae or obviously dirty foreign bodies.
SCOBY is completely black, dry and brittle, and has clearly suffered months of neglect or extreme conditions.
In this type of contamination, what is saved is :
your jars (after thorough cleaning);
your utensils ;
your experience ;
your motivation to start with a healthy strain, for example with a live SCOBY supplied with its starter fluid and clear instructions.
3.2. Cases where the strain is weakened or unbalanced but not contaminated
Conversely, there are situations where the strain is “in difficulty” but not really contaminated:
kombucha which is no longer fermenting, but with no suspect odour;
SCOBY very thin, but normal colour, with no fluffy spots ;
jar left a little too long without sweet tea, but no sign of external microbial attack;
Very acidic kombucha, but clean, with no mould or smell of putrefaction.
In these cases, we’re not talking about dangerous contamination, but about a tired or poorly maintained crop. It is sometimes possible to :
keep a young SCOBY layer;
run a booster test in a small jar;
gradually rebalance the culture.
This is the type of “rescue” we can envisage. It’s a fine line, but it always comes down to two words: food safety.
4. Basic protocol: what should you do if you suspect contamination?
Before deciding what to save, follow a simple observation protocol.
4.1. Step 1: observe calmly
Place your jar in full light (preferably daylight) and observe:
the surface of the liquid ;
SCOBY (top, bottom, edges);
the bottom of the jar ;
the walls.
Search for :
fluffy, coloured patches on the surface;
smooth brown filaments (yeast);
marbled but gelatinous areas.
Mould is mainly found on the surface, in dry or powdery patches. Yeast, on the other hand, forms filaments and gelatinous deposits deep down.
4.2. Stage 2: smell
Gently lift the cloth and smell the inside of the jar:
“Vinegar, cider, apple, yeast, tea” → normal register.
Trust your nose: if the smell puts you off so much that you don’t want to taste it, consider that the strain is not worth saving.
4.3. Step 3: Taste a drop (optional and only if the smell is correct)
This test is only performed if :
no visible mould ;
no unpleasant odours.
In this case, you can taste a tiny spoonful:
if the taste is sweet/tart/vinegary but “clean”, you are probably dealing with a culture that is simply badly adjusted;
if the flavour is very strange, metallic, rotten or aggressive, stop there.
4.4. Step 4: decide
At the end of these three stages, you should fall into one of two categories:
Suspected or proven contamination → throw everything away.
Weakened/unbalanced strain but no sign of contamination → rescue can be attempted.
5. Case n°1: proven contamination – throw everything away, but throw it away properly
This is the least pleasant part, but it’s also the part that protects your health.
5.1. What exactly do you throw away?
In the event of clear contamination (mould, unpleasant odours, insects) :
SCOBY (all nappies) ;
all the liquid in the jar;
any small pieces that might have been put aside elsewhere.
Avoid pouring contaminated kombucha:
in kitchen compost, which you then handle with your bare hands;
directly on your edible plants;
in a blocked sink.
The easiest way is :
flush it down the toilet or sink with a generous stream of water;
or put it in a sealed bin bag.
5.2. Cleaning the jar and utensils
Next, you need to “save” your equipment by cleaning it properly:
Wash the jar inhot water with washing-up liquid.
Pay particular attention to the edges and collar, where spores may remain.
Rinse several times with clean water to remove all traces of product.
Leave to dry in the open air, with the opening facing downwards, or on a clean tea towel.
For utensils (ladle, spoon, funnel) :
same treatment: hot water + washing-up liquid + thorough rinsing.
avoid very worn or smelly sponges, which are themselves breeding grounds for germs.
If you feel more comfortable, you can pour a little boiling water into the jar once it has been washed, then rinse again. This is not clinical sterilisation, but it’s more than enough for domestic use.
5.3. Starting afresh with a healthy culture
At this stage, the best way to “save” your kombucha adventure is to leave with :
a healthy, young, uncontaminated living SCOBY ;
an acidic starting liquid, supplied with the strain;
precise instructions on the quantities of tea, sugar and fermentation time.
This is where a quality culture, sourced from a specialist, makes all the difference: you leave with a SCOBY balanced in yeast and bacteria, and you greatly reduce the risk of further contamination if you follow basic hygiene advice.
6. Case n°2: weakened but probably uncontaminated strain – cautious rescue
If your observation shows that there is no mould or bad smell, but that the :
ferments badly ;
looks “tired”;
gives a flat or fickle kombucha;
then you can try to save the strain itself.
6.1. Separating the SCOBY layers
Often, it is the top, oldest layer that is most damaged.
You can :
wash your hands thoroughly;
Gently peel off the layers of SCOBY ;
observe their colour and texture.
Preferably keep :
a younger, lighter, finer layer that is soft to the touch;
without marked black or brown areas ;
free of doubtful stains.
Throw away the darkest, thickest layers, or those that inspire the least confidence.
6.2. Run a “booster test” in a small jar
To see if the strain is worth keeping, you can test it on a small volume:
Prepare 0.5 L of sweet tea (black or green tea, 25-30 g of sugar for 0.5 L).
Leave to cool completely.
Place your “selected” SCOBY nappy in a clean jar.
Add 50 to 100 mL of very acidic starter liquid (combined from a previous clean batch, if you still have some).
Cover with a clean cloth and a rubber band.
Leave at room temperature, out of direct sunlight.
Over 7 to 10 days, observe :
the formation of a new film on the surface (new mini-SCOBY);
changes in taste (less sweet, more acidic);
the appearance of yeast deposits at the bottom.
If fermentation clearly starts up again, you’ve saved the strain. If, despite good conditions, almost nothing happens, it would be wiser to agree to start again with a new culture.
6.3. Rebalancing parameters
Once the strain has been restarted, you can help it get back into a good rhythm by :
respecting the correct proportion of sugar (around 60-70 g per litre);
ensuring a stable temperature (22-26°C if possible);
Always add enough acidic starter liquid (10-20% of the total volume);
changing the sweet tea regularly (don’t leave the same batch for weeks).
A healthy strain in a stable environment will quickly regain its vigour.
7. Preventing contamination: reflexes to adopt
Saving a stump is one thing. But the ideal is to never have to do it again – or as little as possible.
7.1. Simple, regular hygiene
You don’t need laboratory tools, just a few good habits:
Always wash your hands before touching the jar or SCOBY ;
use clean, well-rinsed glass jars;
thoroughly rinse anything that has come into contact with washing-up liquid;
Use a clean cloth (tea towel, gauze, reusable coffee filter) to cover the jar, secured with a rubber band.
Avoid :
airtight lids during the first fermentation (kombucha needs to breathe);
tea towels that smell musty or greasy;
wooden utensils that are very cracked and difficult to clean.
7.2. Choosing a good location
Your strain will be more stable if the jar is :
away from direct sunlight ;
away from hobs, ovens and radiators;
not stuck to a bin or litter box;
in a place where the temperature remains relatively stable.
A corner of the worktop, away from sources of heat and high humidity, is often ideal.
7.3. Protecting against insects
Gnats love kombucha. To keep them at bay:
use a cloth that is tight enough to keep them out;
monitor regularly ;
Avoid leaving very ripe or rotting fruit right next to it.
A simple, clean cloth held together with a rubber band is often more reliable than a lid with too many holes in it.
7.4. Respect the initial acidity
An acidic environment protects the strain from many intruders.
Always use the starting liquid (kombucha that has already fermented and is very acidic) to start a new batch.
Never fill a jar of sweet tea + SCOBY without this starter liquid.
That’s one of the great advantages of ready-to-use cultures: SCOBY live kombucha comes with its liquid acidified, so you have every chance of getting off to a clean start.
8. Frequently asked questions: whether or not to save a strain of kombucha
8.1. Can I cut off the mouldy part of the SCOBY and keep the rest?
No. Even if the mould is only visible in one area, its spores may already have spread throughout the jar. Cutting away the visible area does not eliminate the risk.
To be on the safe side, we always throw everything away if mould is found.
8.2. My kombucha smells very strongly of vinegar. Is this a contamination?
Not necessarily. A strong vinegar smell generally means that :
fermentation took a very long time ;
the bacteria worked well;
there is little sugar left.
As long as there’s no mould or rotten or chemical smell, your kombucha isn’t ‘contaminated’, it’s just very advanced. You can use it as kombucha vinegar, dilute it or keep it as a starter liquid.
8.3. I’ve used flavoured tea or strange ingredients, is my strain ruined?
Some highly flavoured teas (with essential oils or artificial aromas) or certain ingredients can disturb the strain, make it tired or slow down fermentation. This does not always mean contamination, but :
if the crop does not recover normally afterwards ;
if the batches become capricious ;
It may be simpler to start with a new SCOBY, and reserve your aromatic experiments for the second fermentation in the bottle, rather than at the base of the culture.
8.4. What should I do if I have been infected several times in a row?
If contamination is repeated:
Check hygiene first (jars, cloths, hands);
relocate the jar (perhaps too close to a source of mould);
Replace tea towels or filters with clean, dedicated textiles;
start with a new, balanced crop, with its acidic starter liquid.
Sometimes changing just the strain isn’t enough if the problem is the environment. You have to treat both.
8.5. Can I keep some of the contaminated kombucha to make household vinegar?
Not recommended. Even if you don’t intend to drink it, you would be handling a product potentially loaded with undesirable micro-organisms. For a household vinegar, it’s best to start with an inexpensive classic vinegar, or a very acidic but healthy kombucha.
Conclusion: save what really matters
Saving a contaminated strain of kombucha doesn’t necessarily mean saving this SCOBY at all costs. It’s about :
distinguish between situations where you can revive a weakened crop, and those where you have to throw everything away;
Protect your health by not taking any risks with mould, unpleasant odours or insects;
save your equipment and your habits by setting up a hygiene and observation routine;
if necessary, start with a healthy, well-balanced strain, supplied with its starting fluid and instructions.
Once you’ve got these reflexes down, contamination becomes a rare occurrence. And even if a jar gets lost from time to time, you know exactly what to do: observe, decide, clean, restart.
Your SCOBY is not irreplaceable; what is irreplaceable is your experience and your ability to create an environment conducive to fermentation. With quality cultivation and a few simple steps, your homemade kombucha will cease to be a source of stress and become what it should be: a living, stable, aromatic companion that you’ll enjoy preparing, sharing and drinking, batch after batch.
