Why Kefir Separates & How To Fix It!

When making kefir for the first few times I saw that the milk was always separating into two distinct top and bottom parts. I never quite understood what was going on until I did some research and found out why kefir actually separates:

Kefir separates because the enzymes present in kefir grains coagulate the milk and separate it into whey and curds. When milk is coagulated (or curdled) its casein micelles are destabilized, re-aggregated and immobilized and form the firmer top half of the fermented kefir: the curd.

Although this sounds rather complicated the actual process of kefir separating is actually quite simple. In this post, I’ll go into a bit more details and share with you what I’ve found out from my kefir research 😉

Why does kefir separate?

The reason why kefir separates is that kefir grains contain lactose-digesting bacteria that curdle the milk. These grains are not really grains in the traditional sense of the word but rather live microorganisms that can cause chemical reactions in foods they come in contact with.

When kefir grains are put into milk the lactic acid-producing bacteria (Lactobacillus) contained within start digesting the lactose of the milk and turn it into lactic acid. This process is also called coagulating or curdling the milk and separates it into whey at the bottom and curds on top.

The chart above illustrates the time it takes for milk to separate into whey and curds after rennet has been added. Rennet is simply a group of enzymes found in the stomach acid of many mammals that accelerates this process. Kefir grains work exactly the same as rennet by breaking down lactose.

The chart also shows the rate of firming and highlights the different stages of kefir separation quite nicely:

  1. Casein Isolation: In the first stage, the kefir bacteria isolate the casein particles from the milk and strip any attached water molecules away.
  2. Casein Gel Formation: When most of the casein particles have been isolated they start to aggregate and form a gel-like substance. The more water is separated from the casein the firmer the network of casein particles will become.
  3. Milk Curd Formation: In the third stage the casein particles continue cling together and can form various structures and textures. These are usually visible when you’ve fermented kefir for at least 18-24 hours.

But let’s make all of this more visual. In the video below you can see the exact stages that kefir goes through when separating and if you look closely you can spot the correlation with the three stages as outlines above:

Kefir Separation

Is kefir supposed to separate?

It is completely normal for kefir to separate. The longer kefir is fermented and the longer the kefir grains are left in the milk the more separation will occur. However, separated kefir is still absolutely fine to drink.

There are two main factors that affect if and how soon your kefir starts separating. The main factor is the room temperature but also the ratio of kefir grains to milk can have an impact.

  • High temperatures: Generally, the higher the room temperature the sooner the kefir will separate. This is because the digestive enzymes in kefir become more active as temperature increases. Perhaps you’ve heard that you can store kefir grains in the fridge to take a break. This only works because the activity level of these bacteria is directly influenced by outside temperatures.
  • Amount of kefir grains: The more kefir grains are working on a batch of milk the sooner all the lactose will have been digested and the casein isolated. Think of it this way: the more hungry mouths there are to feed (i.e. kefir grains) the more food you will need (i.e. lactose).

If your kefir has already separated, don’t worry! It’s completely fine to drink but will likely taste sourer than usual. I like to stir the separated kefir with a wooden spoon to mix the whey and the curds and make it easier to strain.

Straining Separated Kefir

However, completely separated kefir is not always what you want. It can also be a sign of over-fermentation and might cause some bitterness or excessive sourness. Luckily, there are a few simple things you can do to prevent kefir from separating!

How do you keep kefir from separating?

To keep kefir from separating, the easiest thing to do is to reduce the fermentation time and drink your kefir fresh. You can also try to adjust the temperature or the kefir grains-milk-ratio and not do a second fermentation.

Here are a few things I’d recommend you try in no specific order:

  • Drink it fresh: If you have been fermenting your kefir for up to 24 hours try reducing the time to 12-18 hours. You can strain your kefir usually as soon as the grains have floated to the top of the milk. To increase the taste and consistency you can always do a second fermentation afterward.
  • Reduce the temperature: Since heat causes the kefir grains to digest the lactose even quicker, a simple solution is to store your fermentation vessel in a cooler place. Of course, that can be quite a challenge in summer if you live without a basement. I always keep mine in the coolest room of the house away from direct sunlight. 74°F (21°C) is a good room temperature to shoot for.
  • Use fewer kefir grains: Perhaps you haven’t even noticed how fast your kefir grains have been growing and multiplying. If you keep using the same batch over and over your bacteria-lactose ratio will soon be out of balance which will cause kefir to separate much sooner. Put some of the kefir grains aside once a week to use for another batch or to eat them. Ever wondered if you can eat kefir grains? Click here to read my article!
  • Skip the second fermentation: When you mature your strained kefir with a second fermentation the separation of whey and milk curds will naturally occur even sooner and is part of the process. You can avoid this by drinking your kefir straight away or storing it in the fridge without maturing it.
Separated Kefir after a Second Fermentation


It may look odd but the separation that occurs in the fermentation process of milk kefir is completely normal. The resulting kefir is also safe to drink and will just taste a little more sour than usual.

To avoid this type of over-fermentation simply reduce the fermentation or room temperature or balance out the kefir grains and milk. One teaspoon for every quarter gallon (half a liter) should do the trick.

Happy fermenting! 😀


  • Hi, I'm Marvin! In early 2019 I started fermenting sauerkraut, kefir, and kombucha and noticed the incredible health benefits that came with it. I was less irritated, had fewer allergies and my skin got better. I started this blog to share how fermented foods have helped me and how simple they are to prepare! Look around and see what speaks to you and all the best on your fermentation journey!

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