How Long do Probiotics Stay in Your System?

Written by: Kari Raman, PharmD, RPh
Published June 29, 2023

How long probiotics stay in your system depends on a number of factors. Some probiotics may never colonize your gut or intestines, so they may never really be active in your system. If you take the right strain of probiotic and take enough CFUs, and take the supplement for long enough, then they may stay at detectable levels in your system for up to three weeks.

I don’t get this question too often at the pharmacy, although I do get this question a lot more about some other substances people might be taking, if you catch my drift. 

So I’ve reviewed the literature that I can find, and will summarize it here. Quick background, I am a licensed and practicing pharmacist, and enjoy answering questions on probiotic supplements. This is my website where I dig into recent research, talk about different species, and offer up helpful tips on how to get the most out of your probiotics.

So let’s dive in and figure out how long probiotics stay in your system.

Studies on length of time probiotics are detectable in your gut

As a general guideline, research suggests that most probiotics, once stopped, will be purged from your system in three to four weeks. This happens because most of the helpful microorganisms do not permanently colonize the human gut. They exert their beneficial effects while passing through the gastrointestinal tract and are then flushed out.

During their transit, they can have numerous beneficial impacts, such as outcompeting harmful bacteria, enhancing gut barrier function, and modulating the immune system. And, some may be detectable for several weeks (in your stool) after you stop taking them.

For example, this study, “Gastrointestinal transit survival of an Enterococcus faecium probiotic strain administered with or without vancomycin,” in the International Journal of Food Microbiology, gave volunteers a specific type of probiotic bacteria. Then, after a treatment period, they stopped the supplementation and regularly tested their poop to see when the bacteria was no longer around. Their research found:

Three weeks after cessation of probiotic product intake, the E. faecium strain could not be detected in faeces in any of the subjects suggesting that this strain was either washed out or in numbers below the detection limit.

So, in this study, three weeks was the maximum limit of how long they stayed detectable after the treatment was stopped. 

In another study, a helpful bacteria – bifidobacterial – was given to volunteers. The researchers took regular stool samples, and found that the levels of the probiotic started dropping four days after the supplementation stopped, and then was completely out of the system – undetectable – eight days after stopping. So, in this case, probiotics stayed in the system for seven days and were undetectable eight days after the last dose. 

Answering a related question:

How long do probiotics stay in your intestines?

The studies I reference above should also apply to the question of how long the probiotics stay in the intestines, and the answer is going to be at most three to four weeks. After that, if you’ve stopped taking the supplement, you are unlikely to have any detectable level of the microorganisms. The studies I cited are for people who took probiotics for an extended period of time – if you only took one or a couple of doses, I’d bet that they would leave your system within a few days. If you took a dose or two, and then are having serious digestive problems that are not resolving, visit your doctor.

How long do they stay in your system after stopping taking them?

This is going to depend on how long you’ve been taking them. If you’ve been regularly taking the supplements, then the bacteria/yeasts/etc. are going to stay in your gut for, at most, about three weeks. If you’ve only taken a dose or two for a day or two, I’d expect them to leave your system quickly, after just a few days. Remember that they can cause some bloating and gas when you first start supplementation, and this may last for the first few days of supplementation. If you start taking a particular strain or brand, and just can’t stand how it makes you feel, and then you stop after a couple of days of supplementation, I’d expect the probiotics to leave your gut within just a few days. If your gut doesn’t return to normal after a few days of stopping the supplement, talk to your doctor to make sure that there isn’t another, underlying condition that needs to be treated.

How you can help have a healthy microbiome

It actually seems a little depressing that probiotic supplements don’t stay active in the gut for very long after you stop taking them. Thankfully there are other steps you can take to help have a healthier gut microbiome. The biggest one, for otherwise healthy people, is to focus on having a healthy diet.

A healthy and diverse gut microbiome plays an important role in your overall health. This complex community of microorganisms helps with digestion, protects against disease-causing bacteria, and even influences your mood and mental health – read my piece on how research suggests that they might actually help make you happier.

Fiber and prebiotic foods play a vital role in maintaining this ecosystem in two primary ways:

1. Nourishment: Prebiotics are non-digestible food components, usually fibers, that act as a food source for the beneficial bacteria and other species in your gut’s microbiome. Prebiotics help to stimulate the growth and activity of these beneficial bacteria. Examples of prebiotic foods include garlic, onions, asparagus, bananas, oats, apples, flaxseeds, seaweed, and many other fruits, vegetables, and whole grains. Basically, it’s healthy bacteria food for feeding the healthy bacteria in your intestines. 

2. Regular Bowel Movements: It turns out, regular pooping is good. A high-fiber diet also helps to maintain regular bowel movements, which can help prevent constipation and promote a healthy digestive tract. Soluble fiber, which absorbs water and softens the stool, can be found in oats, peas, beans, apples, citrus fruits, carrots, barley and psyllium. Insoluble fiber, which can add bulk to the stool and help food pass more quickly through the stomach and intestines, can be found in whole wheat flour, wheat bran, nuts, beans and vegetables, such as cauliflower, green beans and potatoes.

A balanced diet, rich in fiber and prebiotic foods, is essential for a healthy gut microbiome. It’s also important to remember to drink plenty of water, as fiber absorbs water and can lead to constipation if you’re not properly hydrated. While I wasn’t able to find any research on how long probiotics stay in your system based on the food you eat, I’d have to bet that eating a diet rich in fiber and other prebiotics can help good probiotics colonize your gut and stay in your system. 

Note: It’s always best to seek personalized advice from a healthcare provider or a dietitian, as individual needs can vary based on age, health conditions, lifestyle, and other factors.

What are Probiotics?

Now that we’ve talked a bit about how long probiotics stay in your system, let’s talk a bit about what they actually are. I get asked basic questions by patients all the time at the pharmacy, and most around how they are supposed to improve gut health. So, what do I tell patients about them at the pharmacy counter?

Probiotics are live microorganisms that might offer health benefits when consumed in appropriate amounts. These microorganisms, mostly bacteria but also yeast, are believed to promote gut health and overall well-being. The human gut is full of bacteria, yeasts, fungi and other living organisms, usually referred to as the gut microbiome. Keeping this microbiome is essential for staying healthy, but given our modern (and rather unhealthy lives) that isn’t always easy for everyone. 

The term “probiotic” comes from Latin and Greek words meaning “for life.” This name underscores the potential role these beneficial bacteria play in supporting health. They’ve been associated with a range of potential health benefits, including:

Digestive Health: They might help maintain the balance of good and bad bacteria in the gut, a balance believed to be crucial for digestion, nutrient absorption, and bowel regularity. I’ve read enough clinical study reviews (like this one) to think that for some people, the right supplements can be helpful. But the trick is figuring out if there are any ones that are good for your specific situation! 

Immune System Support: A significant part of our immune system is located in the gut. They might help strengthen the intestinal wall, reducing the chance of harmful substances entering the bloodstream, and potentially modulating immune responses.

Mental Health and Mood: The connection between the gut and brain, often referred to as the gut-brain axis, involves bidirectional communication. Some studies suggest that certain probiotics may help reduce symptoms of depression and anxiety through this link. I’ve written on the question of “can probiotics make you feel happy” here, where I cite some research on this link. 

Protection against Pathogens: The right bacteria and yeasts living in your gut might inhibit the growth of harmful bacteria by producing substances like lactic acid, which could make the gut less hospitable for some pathogens. 

You don’t have to purchase supplements to get them! They can be found in various fermented foods like yogurt, kefir, sauerkraut, kimchi, and miso. Of course, they are also available as dietary supplements. Different strains of probiotics serve different purposes, so it’s essential to choose the right type based on your health concerns.

With our focus on “how long do probiotics stay in your system?”, understanding what they are and how they function provides a clearer picture of their temporary nature in our bodies and how they clear out if you stop taking them. They offer many potential benefits during their stay, but their duration in our system can vary based on several factors.

So, when considering adding supplements to your wellness routine, keep in mind that these tiny organisms work diligently to support your health, even if they might not be in your system for very long.

Another article that might interest you

Fasting and Its Impact on Probiotics

I’ve written an article on the connection between fasting and probiotics. Fasting can foster beneficial gut bacteria growth, potentially enhancing the effectiveness and longevity of probiotics in the body. There isn’t as much research on how to combine these two strategies, but what little research there is seems to indicate that you can add the supplement to your fast and help improve your gut health – without breaking your fast!

Apple cider vinegar

Some patients have asked me at the pharmacy counter if they can take probiotics while they are using apple cider vinegar. The answer is yes, but in my article on the two I talk a bit about how the timing of when you take each matters.

Pharmacist Kari Raman

I’m Kari Raman PharmD, RPh, and I am a licensed, practicing pharmacist. I hold a Doctorate in Pharmacy from The University of the Pacific, and I’ve served patients in retail, compounding and hospital pharmacies.

Probiotics are confusing!

One of the most common questions I get asked by patients is about probiotics. And the truth is, probiotics are not as well understood by the healthcare community as they should be.

So I’ve been reading a lot of probiotic clinical trials, and sharing what I’m learning here.

I hope Pharmacist Probiotics helps you find out if there is a type of probiotic that works for you!