Kefir vs yoghurt: Which is better for your gut health

Fermented dairy foods are often recommended for gut health because they contain naturally occurring beneficial bacteria that support digestion and the immune system. Kefir and yoghurt are two of the most popular options, and while they are similar, they are not the same thing. 

Neither is universally “better”. The right choice depends on how active your gut is, how sensitive you are to dairy, and what your goals are for including fermented foods in your diet. 

Doctify can connect you with vetted GPs who can help you decide which foods are most suitable for your specific health needs.

Why gut health matters

The gut microbiome plays a key role in digestion, immunity, inflammation control, and even the regulation of your mood. A balanced mix of gut bacteria helps break down food efficiently and protects the gut lining.

Probiotics are live microorganisms that can support maintaining that balance. They work best when consumed regularly rather than occasionally, which is why foods like yoghurt and kefir can be useful and easy inclusions to everyday meals.

What is yoghurt?

Yoghurt is made by fermenting milk with specific bacterial cultures, most commonly Lactobacillus and Bifidobacterium strains. These bacteria help convert lactose into lactic acid, giving yoghurt its characteristic texture and taste. 

Natural and Greek yoghurts tend to contain live cultures, compared to the flavoured versions, which often have added sugar and fewer probiotic benefits.

What is kefir?

Kefir is made using kefir grains, which contain a mix of bacteria and yeasts. This process usually results in a product that has a wider variety of microbes than yoghurt. 

Kefir has a thinner, drinkable consistency and can be made from dairy milk or alternatively with sugar-based drinks, water, fruit juices or vegetables. Due to its microbial diversity, kefir is often more potent, although this does not necessarily mean that everyone’s digestive system tolerates it better.

Probiotic content: Kefir vs Yoghurt

Whilst both yoghurt and kefir have probiotic properties, there are some differences. Kefir often provides a greater diversity of bacterial strains and yeast species.

However, more strains are not always better for everyone, especially for people who have sensitive digestive systems. Some people with sensitive digestion or who have IBS-type symptoms may find that a simpler probiotic profile may be easier to tolerate. Live cultures are also key, so heat-treated or long-life products may offer fewer benefits regardless of whether they are in yoghurt or kefir. 

Digestibility and lactose tolerance

Both yoghurt and kefir contain less lactose than milk because the process of fermentation breaks lactose down. Many people who struggle with consuming milk may find fermented dairy easier to tolerate.

Some people tolerate kefir better than yoghurt because its microbes continue to break down lactose even after consumption. Other persons may have a more sensitive response to kefir, showing that individual responses may differ. 

Effects on common gut symptoms

When starting fermented foods, mild bloating, wind or changes in bowel habits can happen at first. This is often temporary and reflects the gut microbiome adjusting.

Starting with small amounts and increasing gradually helps the gut to adapt to the foods and can minimise discomfort, especially for those people who are prone to IBS or those with sensitive digestive symptoms. 

Nutritional differences

Yoghurt, especially Greek yoghurt, is typically higher in protein and can be more filling. Kefir tends to be lower in its protein content but greater in its microbial diversity. 

Both provide calcium, B vitamins and beneficial fat, but are dependent on the type used. Added sugars in flavoured versions of both can reduce the gut health benefits, so the plain varieties are usually the healthier and better choice for most people.

How to choose the right option for you

If you prefer thicker textures and higher protein, yoghurt may be the better fit for you. If you are looking for more probiotic exposure and prefer a drinkable option, kefir may be more appealing.

Taste, convenience, cost, and how your body reacts are just as important as their nutritional content when choosing between the two. 

How to introduce fermented dairy safely

It is recommended to start with small amounts, such as a few spoonfuls of yoghurt or a small glass of kefir. This can then be gradually increased over several days.

If symptoms worsen or persist, it may be better to pause or switch to the other option. Persistent discomfort is not something that people should push through. 

When to speak to a GP

You should seek medical advice if you have ongoing bloating, abdominal pain, or bowel changes despite modifying your diet. A GP can also help assess suspected lactose intolerance, a dairy allergy or digestive symptoms associated with weight loss, fatigue or anaemia.

Doctify can help you find qualified GPs in your area who can help navigate your unique situation and provide tailored advice for your dietary and health goals.

Final thoughts

Both kefir and yoghurt can support gut health once they are tolerated well. Consistency and individual response matter more than choosing the “best” option. 

If gut symptoms persist or if symptoms are unclear, a GP can help guide personalised choices that support digestive health without introducing restrictions.

Find the best general practitioners in the United Kingdom, or search for trusted experts globally:

• General Practitioners in Ireland
• General Practitioners in Australia
• General Practitioners in the United Arab Emirates
• General Practitioners in Germany

Medically Reviewed
Last reviewed on 06/01/2026