Fruit Flies in Kombucha -How to Save the Booch!

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What to do if you find fruit flies in Kombucha! I know your first impulse is to throw it away, but stop! let’s not be hasty. You can save your Kombucha & SCOBY!

Images of a SCOBY being removed because fruit lies in Kombucha

Can your Kombucha be saved if you find fruit flies??

The first time I found fruit flies in my Kombucha I nearly vomited. There were fruit flies everywhere and maggots wriggling around. I just wanted to throw the lot on the back garden. Unfortunately, I didn’t have a SCOBY hotel and that would have been the end of my Kombucha brewing days. I had bought my SCOBY and had no backups.

What do you do if you find Fruit Flies in Kombucha?

First of all breath and relax. If you find a fruit fly infestation in your brew you have a few options. The choice you make will depend on a few things;

  • Do you have a well stocked SCOBY hotel?
  • Are you squeamish when it comes to fruit flies and their maggots?
  • How thick are the SCOBY layers in the brewing vessel?
  • Is it an infestation or just a few fruit flies and some wriggles?

1 -You have a well stocked SCOBY hotel

Woohoo! You have a well-stocked SCOBY hotel you can just throw away the batch of Kombucha and use a SCOBY from the hotel. To ensure you don’t contaminate the next brew you will need to thoroughly clean the Kombucha vessel.

How to Clean Your Kombucha Brewing Vessel

  1. Completely pull apart all pieces of the vessel.
  2. Remove the tap and all of the seals.
  3. Thoroughly wash all parts with warm soapy water.
  4. Ensure that soapy water flows through the tap and any ooglies are removed.
  5. Rinse off all vessel pieces.
  6. Pour non-chlorinated water over pieces to remove soap and chlorine.
  7. Put together your brewing vessel.
  8. Begin a new Kombucha brew

2 – If you’re squeamish when it comes to fruit flies and their maggots?

If you’re in the number 2 boat, I suspect you will need to throw away the Kombucha and start again. Whilst the booch probably can be saved, if you think you will be unable to handle the SCOBY with the maggots then you may need to throw the lot. Moving forward please read the article on how to prevent fruit flies in your Kombucha.

Kombucha brewing croc with plastic tap and cover to keep away fruit flies

Also, take a look at this Kombucha brewing vessel. The tight fighting cloth is the first step to not having to worry about fruit flies in the future!

If you’re looking for a supplier of a new SCOBY take a look here. Alternatively, you could join our FB page and ask if anyone has a free SCOBY they can send you.

Make sure to clean you Kombucha brewing vessel as per the method above prior to starting a new brew.

3 – How thick are the SCOBY layers in the brewing vessel?

If you’re at number 3 you don’t have SCOBY in reserve and you’re not squeamish about the fruit flies. This is great! So we need to take a close look at the SCOBY layers. How thick are they and how many layers are there?

When I got my first infestation I had about 6 thick layers. I should have already transferred some to a SCOBY hotel but I hadn’t.

If you have a thick layer of SCOBY you have a very good chance of successfully saving your brew. The SCOBY acts like a barrier and the fruit flies won’t have been able to go all the way through to the bottom layers and into the Kombucha.

Close up picture of SCOBY on a white background, Kombucha in the background

If you have a thick SCOBY layer and Fruit Flies!

  1. If you have a tap on your vessel remove as much of the Kombucha as you can without disturbing the liquid within about 2cm or 1 inch of the bottom SCOBY.
  2. Reserve the liquid and put a lid or clean towel over it.
  3. Open the top of the vessel and remove each layer of the SCOBY and put in a separate clean dish.
  4. As you do this line the dishes up in order so you know which layer was from the top (most infested, down to the bottom layer… probably safe.)
  5. Be very careful when removing the layers not to tip the SCOBY or liquid onto the layer below as much as possible.
  6. Once this is complete and there are no more SCOBY in the brewing vessel, examine the SCOBY to determine which levels need disposing of.
  7. Throw away all contaminated SCOBY immediately.
  8. I usually also throw away one more layer to be safe. Alternatively, you can start a separate SCOBY hotel with the unknown layer. Add 1/2 cup of reserve kombucha from step 2 and 1 cup of sweet tea as per normal. You will know within 2 days if there were any fruit fly lava in the SCOBY.
  9. Hopefully, you have at least one maybe to SCOBY left to continuing brewing.
  10. Cover the remaining “safe” SCOBY so any random fruit flies don’t infest them.
  11. Wash the brewing vessel using the method above.
  12. Choose the SCOBY that was furthest away from the fruit flies and add it to the cleaned vessel with 2 cups of starter kombucha and some brewed tea to refill the vessel. Use this Kombucha guide.
  13. If you have leftover SCOBY and kombucha it won’t hurt to place it all in a large jar with a cloth over it, add some tea and see what develops.

Within a few days, you will know if you’ve successfully saved your Kombucha from fruit flies.

If you have a thin SCOBY layer and Fruit Flies!

This is tough! If there isn’t a thick SCOBY there is a chance you will have wrigglers swimming in your booch.

    1. Find a clean glass jar.
    2. Without disturbing the brewing vessel take a cup (or a little more) of Kombucha from the vessel. Be careful not to take liquid from within 3cm of the SCOBY.
    3. Add 1/2 cup of sweet tea to the jar.
    4. Cover with a tea towel and elastic band.
    5. In 2 days check for fruit flies. If there are no fruit flies leave the brew undisturbed for a week or until there is a decent SCOBY present.
    6. Clean the brewing vessel as per method above.
    7. After a week restart your brewing using my Kombucha guide and the jar of saved SCOBY and starter.

If you found fruit flies in the jar on day 2 you will have to throw away the booch and start again with a clean vessel and new SCOBY.

If you’re looking for a supplier of a new SCOBY take a look here. Alternatively, you could join our FB page and ask if anyone has a free SCOBY they can send you.

Is it an infestation or just a few fruit flies and some wriggles?

Even if you have an absolute infestation you can still get a clean bill of health with your SCOBY and booch. Just choose the method above which suits your circumstances. Do you have a thick SCOBY layer or a thin SCOBY layer?

I hope I have helped you to save your Kombucha and to feel safe in doing so. You will not be drinking any of the Kombucha until enough time has passed to reassure yourself that there is no longer anything unwanted living in your drink.

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Thanks for reading all the way through to the end. I really hope I have helped you with your brewing journey. Feel free to leave any comments or questions below 🙂

4 thoughts on “Fruit Flies in Kombucha -How to Save the Booch!”

  1. Brittany says:

    Hi! I have a THICK SCOBY and just found a couple fruit flies inside the rim of my jar 🙁 I took them out immediately! They were still alive, none have been in there long enough to drown. What is your suggestion for saving my booch?

    1. Julie Carlyle says:

      Hi Brittany
      If you drain off a cup of the Kombucha and cover it with a cloth tied closed it will start to produce a new SCOBY. This can be your backup in case you haven’t saved your batch. You will be able to use this as a starter.

  2. Emily Quindry says:

    This was SO helpful- thank you!!!

  3. Candyce R Shuford says:

    Great tips thank you!

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