Can stopping probiotics cause problems?

When you take probiotic supplements, the benefits don’t last long. This is because your gut needs a steady supply of good bacteria and the foods that nourish them in order to thrive.

There have been no rigorous scientific studies that look specifically at what happens when healthy individuals stop taking probiotics.

However, if you stop populating your gut with “good” bacteria — either through supplements or food — the delicate balance can be disrupted and “bad” bacteria may begin to take over.

Probiotic supplements can be beneficial for people with certain medical conditions, such as high cholesterol and irritable bowel syndrome (IBS). Your doctor might also recommend taking probiotics if you are currently taking antibiotics.

For most people, however, there is no evidence that probiotic supplements provide any benefits. The bacteria from a supplement likely take up residence in your gut, but scientists have found that the effects wear off within 1-3 weeks after you stop taking them. 

At ZOE, we believe that the best sources of probiotics are the foods you eat. By incorporating fermented foods and plenty of plant foods into your daily diet, you ensure that the “good” microbes in your gut can thrive.

ZOE runs the largest study of nutrition and the gut microbiome in the world. Our research has identified 15 “good” gut bugs linked with better health and 15 “bad” bugs linked with worse health. 

The ZOE at-home test analyzes your gut microbiome and tells you which of the 15 “good” and 15 “bad” bugs are in your gut and which foods to eat to improve your gut health. 

Read on to learn about what happens when you stop taking probiotics and what you can do to lessen any negative effects.

What are probiotics?

Probiotics are living microbes that scientists believe can affect the health of your gut microbiome. The delicate balance of bacteria in your gut plays a role in a huge range of other bodily functions and systems, from your immunity to your mental health.

You can buy probiotic supplements in liquid or pill form. You can also easily acquire them through your diet, since probiotics occur naturally in many fermented foods. 

Probiotics occur naturally in:

  • yogurt

  • Parmesan, aged cheddar, Swiss cheese, and cottage cheese with live cultures

  • kefir

  • kimchi

  • sauerkraut

  • miso

Not all store-bought fermented foods contain probiotics — make sure you look for ones that specifically contain live cultures. Many yogurts, for example, contain no probiotics and are very high in refined sugar.

Most probiotic supplements that you can buy contain bacteria that are easy to grow. They are not necessarily those that give you the most benefits. Many of them also only contain one or a few different types. 

Everyone’s gut microbiome is totally unique, making it challenging to predict which probiotic supplement is best for each individual. 

ZOE research doesn’t focus on single types of bacteria. Instead, we focus on foods that support the 15 “good” bugs and suppress the 15 “bad” bugs, many of which you can’t buy as a probiotic supplement. 

Having more of the 15 "good" bugs is good for your overall health. Eating food that benefits your unique microbiome can help your "good" bugs thrive.

What are the benefits of probiotics?

Probiotic bacteria are good for your gut health, which is important for your overall health. They may be particularly beneficial in specific circumstances, such as when you’re taking antibiotics for an infection or as a preventative measure before or after surgery. 

There is limited data, however, on the benefits of probiotic supplements in otherwise healthy people. 

The results of taking probiotics vary widely, depending on the type of bacteria, the quantity of specific bacteria in the supplement, and the health of the individual.

Other factors that can change the results include the age of the supplement — many probiotics become ineffective over time — and how a person stores it. It’s worth checking the manufacturing label to find out how to best store a probiotic product. 

A 2018 scientific review found that in otherwise healthy adults, probiotic supplements could:

  • temporarily improve levels of specific “good” bacteria in the gut microbiota

  • boost immune system responses

  • help regulate stool consistency and bowel movements

  • improve the concentration of the “good” bacteria Lactobacilli in the vagina

Since everyone’s gut composition is different, these effects are not the same in everyone.

What happens when you stop taking probiotics?

We asked Dr. Will Bulsiewicz — gastroenterologist, gut health expert, and author of Fiber Fueled — to explain what happens when you stop taking probiotic supplements.

“[It] depends on your individualized response to the probiotics and what happened when you started them in the first place,” Dr. Bulsiewicz said. 

“Probiotics are a bit difficult to predict because they're a bit like a foreign exchange student arriving in a high school. The cliques are already established, and then this new person walks in and it's possible that they change the dynamics, but it's also possible that nothing changes at all.” —Dr. Will Bulsiewicz

It’s difficult to predict how you respond to a probiotic because no two people’s gut microbiome is the same. There may be benefits, harms, or no changes at all. 

That’s why it’s wise to think about whether they made any difference for you, specifically.

Did your digestion improve? It might get worse again if you stop. Did you get over that cold faster than usual? Maybe they’re helping your immune system. Did you feel no different than before? Then stopping might not have any effect either.

Dr. Bulsiewicz recommends having a specific goal in mind before starting probiotic supplements. “[W]hen I recommend probiotics in my gastroenterology clinic, I always have a specific goal in mind,” he explained.

“Are we treating IBS, gas and bloating, or constipation? If so, then I can choose the probiotic most likely to address that specific issue, and we can make an assessment of whether or not the symptom improves while on the probiotic.”

There is a good chance that what happens when you stop taking probiotics is linked to why you started a supplement in the first place. 

“If a person improves while on a probiotic, then there is a strong possibility that they will see worsening of their digestive symptoms when they stop the probiotic,” said Dr. Bulsiewicz.

“If, alternatively, that person never really improved on the probiotic in the first place, then they likely won't notice a difference whether they continue the probiotic or stop it,” he added. 

What happens when your gut is not in balance?

If your gut microbiome is out of balance, your body is more prone to some illnesses and diseases. The medical term for this imbalance is dysbiosis.

Acute symptoms you might notice include:

  • gas

  • nausea

  • bloating

  • fatigue

  • diarrhea, constipation, or both

While all of these are common symptoms and happen to most people from time to time, chronic digestive issues could be a sign that your gut bacteria are not able to digest your food properly. 

There is no one-size-fits-all fix for these issues, but changing your diet to be more gut friendly can have a big impact. 

With the ZOE program, you find out which foods work best for your metabolism and your unique gut microbiome to help your “good” bugs thrive.  

Spend money on good quality food, not pills

At ZOE, we believe that you can get everything you need for a healthy gut from the foods you eat.

You can make your diet more gut-friendly permanently by regularly including fermented foods and high-fiber foods. Unlike stopping and starting supplements, the benefits of changing your diet are long-term. 

Supplements have limited effects in healthy people, and experts do not have a stance for or against using them. Some health experts warn that claims about probiotics on the whole can be misleading.

To reap the benefits, you have to consume probiotics while the bacteria are alive, but researchers note that some probiotics in supplements die during their shelf life, or even en route through the stomach.

If you’re not taking probiotic supplements for a specific medical reason and are looking to improve your health, try changing your diet instead. Getting probiotics from food will also ensure that you get a diverse range of bacteria, rather than loading up on a few strains.

In addition to the fermented foods listed above, aim to eat around 30 different plant foods each week, including vegetables, fruits, spices, nuts and seeds, legumes, and whole grains. Plants are high in fiber, antioxidants, and prebiotics, which help feed those “good” gut microbes. 


If you experienced significant benefits from taking a probiotic supplement, these benefits will likely go away soon after you stop using them. Likewise, if the probiotics had no effect, stopping them will be similarly uneventful. 

While probiotic supplements have been scientifically proven to be useful for people with specific medical needs, otherwise healthy people can get their probiotics from their diet.

A healthy gut microbiome is one with a diversity of “good” bacteria. A diet rich in fermented foods and fiber-rich plants will feed these “good” microbes and can have an overall positive effect on your health. 

Dietary changes are long-term shifts, meaning they can have longer-lasting results than taking a course of probiotic supplements.

If you want to learn more about which microbes live in your gut and how to encourage the “good” ones to grow, take our free quiz today. 

The ZOE at-home test uses the most advanced technology available to analyze your gut microbiome and help you find the best “gut booster” foods for your body that help the 15 “good” bugs thrive in your gut. 


A review of probiotic supplementation in healthy adults: helpful or hype? European Journal of Clinical Nutrition. (2018).

Beneficial effects of dietary polyphenols on gut microbiota and strategies to improve delivery efficiency. Nutrients. (2019).

Dysbiosis. The Theory of Endobiogeny. (2020).

Probiotics: Fact sheet for health professionals. (2020).

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Medicine. (2016).

The impact of dietary fiber on gut microbiota in host health and disease. Cell Host and Microbe. (2018).

The pros, cons, and many unknowns of probiotics. Nature Medicine. (2019).

You are what you eat: diet, health and the gut microbiota. Nature Reviews Gastroenterology & Hepatology. (2018).