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Can You Take Probiotics With Antibiotics? Yes, Here’s How

Written by Dr. Michael Ruscio, DC on June 23, 2025

Written by Dr. Michael Ruscio, DC on June 23, 2025 — Reviewed by Hannah Wright

• Probiotics With Antibiotics: What Happens?|
• Antibiotic Side Effects|
• How to Take|

If you’ve been prescribed antibiotics, you might be wondering: Can I still take my daily probiotic? The short answer is yes—and in many cases, you should.

It might seem counterintuitive to add bacteria to your body when you’re sick or fighting an infection that you’re treating with antibiotics. After all, antibiotics are designed to kill bacteria—so wouldn’t probiotics just get in the way? And isn’t it a waste of probiotics if you’re just going to kill them with antibiotics? 

These ideas sound logical in theory, and I’ve heard them echoed by both patients and healthcare providers. But when we look at the body of research, these concerns don’t hold up.

Older or smaller studies have questioned the benefits of taking probiotics during antibiotic therapy 1. But broader, more rigorous research—including dozens of clinical trials and meta-analyses—paints a very different picture.

Probiotics can not only support gut recovery during and after antibiotic use, but they can also help reduce common side effects like diarrhea and bloating.

Let’s break down what research shows about combining probiotics with antibiotics, which strains are most effective, and how to use them for maximum benefit.

What Happens When You Combine Probiotics and Antibiotics?

A common concern when taking probiotics with antibiotics is that the antibiotics could eliminate both harmful and beneficial bacteria and simply wipe out the probiotics—what a waste! 

However, human research indicates that some probiotic strains can survive this environment and provide health benefits when we take them during antibiotic treatment.

Let’s look at some examples from research. 

Probiotics and Helicobacter pylori Infection

An umbrella study of many meta-analyses (studies of studies) found that people who take probiotics and antibiotics together for an H. pylori infection (of the stomach) typically have better results than those who take antibiotics only 2. In fact, adding higher doses of multi-strain probiotics to antibiotics can increase the success of getting rid of H. pylori by 13%.

These benefits might happen because probiotics can 3:

• Make substances that slow bacterial growth
• Take up space on the stomach lining and block H. pylori from attaching
• Use an enzyme to prevent H. pylori from sticking
• Strengthen the stomach’s protective barrier
• Reduce side effects from antibiotics, making it easier for people to finish taking them

Probiotics and SIBO

If you have a small intestinal bacterial overgrowth (SIBO), taking probiotics with antibiotics may also make treatment more effective than antibiotics alone. For example, the following clinical trials suggest that:

• Adding Saccharomyces boulardii (a probiotic yeast), an herbal supplement, and glutamine to a SIBO treatment of antibiotics and a low FODMAP diet may improve symptom relief, especially for people with methane-predominant SIBO (intestinal methanogen overgrowth) 4.
• Taking S. boulardii with the antibiotic metronidazole may be more effective at clearing SIBO than taking metronidazole alone 5.
• Combining probiotics and antibiotics may clear SIBO in almost 9 out of 10 people with SIBO and Crohn’s disease 6.

Additionally, probiotics may be the key to overcoming hydrogen sulfide SIBO, especially in people who haven’t responded to antibiotics 7.

Probiotics and Clostridium difficile Infections 

Probiotics are also promising for people with serious Clostridium difficile infections, which are often caused by taking too many antibiotics 8.

C. difficile is a tenacious bacterium that takes advantage of disruptions in the gut microbiota. It can be very difficult to kill and can lead to life-threatening diarrhea and colon inflammation 8.

Probiotics can safely prevent C. diff infections in both adults 9 and kids 10. Limited research suggests they may also be able to help get rid of an active C. diff infection 11.

Probiotics and Genital Infections

Probiotics are effective at curing and preventing bacterial vaginosis (an overgrowth of bacteria in the vagina), especially when taken with antibiotics 12.

And in men with infections of the genital tract, probiotics added to antibiotics have been associated with higher infection clearance rates than antibiotics alone 13. 

Probiotics Help Prevent Antibiotic Side Effects

Probiotics may help restore balance to the gut microbiome and combat antibiotic side effects, according to high-quality research. 

Antibiotics work by killing harmful bacteria that cause infections. Most antibiotics are broad-spectrum, meaning they kill many types of bacteria, whether they’re helpful, neutral, or harmful. Some broad-spectrum antibiotics, like amoxicillin, ciprofloxacin, and cefprozil, can alter the gut microbiome for up to 12 weeks 8. 

When we take antibiotics, they get rid of the invaders (harmful bacteria), but they also kill healthy gut flora in the process. Losing beneficial bacteria during antibiotic treatment can cause dysbiosis (microbial imbalance) and its downstream effects, including 8:

• Reduced microbial diversity: Many helpful species are depleted and may not fully recover.
• Loss of key species: Bifidobacteria and other beneficial microbes often take the biggest hit and recover slowly, if at all.
• Increased antibiotic resistance: Disrupted microbiomes tend to harbor more resistant bacteria and resistance genes.
• Overgrowth of harmful microbes: Some antibiotics encourage the rise of species linked to inflammation or illness. 

So, when we take an antibiotic, especially for a longer length of time or repeated rounds, we may experience some unpleasant side effects, such as diarrhea, a yeast infection, or gastrointestinal pain or bloating.

Probiotics and Dysbiosis 

Dysbiosis, a common negative effect of using antibiotics, impairs normal gut function and allows harmful bacteria to increase rapidly. Dysbiosis can contribute to diseases—like ulcerative colitis, Crohn’s disease, and C. diff infections—that cause serious symptoms 14.

Adding probiotics, such as Lactobacillus species, Bifidobacterium species, and S. boulardii, during antibiotic treatment may help maintain a healthy balance of gut microorganisms and support the recovery of beneficial microbes 15.

In fact, a systematic (methodical) review of studies showed that about 8 of 10 (83% of) healthy people who took antibiotics had their gut bacteria recover when they also took probiotics 16. 

However, not all research agrees. A more recent meta-analysis of five randomized controlled trials found that taking probiotics with antibiotics didn’t reliably protect or restore bacterial diversity, especially for most healthy people 17. 

How does this make sense if other good studies have shown positive effects when taking probiotics with antibiotics? The researchers suggested that taking probiotics may help prevent diarrhea or C. difficile infections during antibiotic use—especially in people at higher risk—but this benefit doesn’t seem to come from protecting the gut microbiome’s overall balance or diversity 17.

In other words, the protective effects may be related to something other than the bacteria probiotics leave in your gut microbiome, and we have yet to find out what that is. At this point, the evidence that probiotics might help restore gut bacteria after antibiotics is mixed.

Probiotics and Antibiotic-Associated Diarrhea

Diarrhea is one of the most common side effects of antibiotic use, and it’s generally caused by dysbiosis. Probiotics can help prevent antibiotic-associated diarrhea in people of all ages 18 19.

A meta-analysis found that taking probiotics with antibiotics may reduce the risk of antibiotic-associated diarrhea in adults by more than a third (37%). High doses of probiotics may be even more effective, possibly reducing the risk by almost half (46%) 20. This robust evidence supports the protective effect of probiotics during antibiotic therapy.

Higher doses of probiotics can also prevent antibiotic-associated diarrhea or reduce its duration in children by a whole day 21.

The earlier probiotics are added to antibiotics, apparently the better. Studies have shown that:

• Starting probiotics within 24 hours of starting antibiotic treatment can reduce the risk of diarrhea by 35% in children 18.
• Starting probiotics within 48 hours of starting antibiotics can reduce the risk of antibiotic-associated diarrhea by 29% in elderly people 19.

Unfortunately, starting probiotics later than 48 hours after your first antibiotic dose may not reduce the risk of diarrhea 19. But if you miss the 48-hour window, it’s still probably a good idea to start probiotics during your antibiotic treatment because they may still help the antibiotics do a good job. 

As always, make sure to consult a knowledgeable healthcare practitioner when trying any new supplements.

How to Take Probiotics With Antibiotics 

For my clients who need to take antibiotics, I advise them to add probiotics as soon as they start taking antibiotics. 

It might even be better to start probiotics before a course of antibiotics and continue them for a while after the antibiotic therapy is complete. I think of this approach like priming the pump to help keep antibiotic side effects like diarrhea at bay and giving the gut microbiome a better chance of recovering 22.

What’s the Best Probiotic To Take With Antibiotics?

Most probiotic products fit into one of three categories:

• Lactobacillus/Bifidobacterium blends
• Saccharomyces boulardii
• Soil-based species (Bacillus species)

All of these have shown benefit when used alongside antibiotics, so there’s no need to go strain shopping 23. This is because all probiotics tend to have the same health benefits, such as 24:

• Balancing the gut microbiota
• Regulating the immune system
• Reducing inflammation
• Fighting infectious organisms
• Reducing leaky gut

Not only are all three strains helpful, but taking all three together is likely the most effective antibiotic support 2. Most research trials use a blend of probiotic strains, and that approach works well for us in the clinic. We encourage our clients to use what we call probiotic triple therapy, which is simply taking all three categories together. 

When Should You Take Probiotics?

Some would recommend taking probiotics at least two hours before or after antibiotics to maximize the benefit.

It’s ok to do this, but if that makes the medication schedule too complicated, we just have our clients take them at the same time. It’s better to take probiotics and antibiotics together than not to take them at all. 

What About Probiotic Foods?

The diet is another way to add probiotic bacteria to the gut. A number of fermented foods, such as kefir, kimchi, kombucha, lacto-fermented sauerkraut, and many types of yogurt, are rich in healthy bacteria.

However, as this table shows, it may be difficult to eat enough fermented foods to get the range of species and the therapeutic dose you’ll find in a probiotic supplement 25 26 27.

Eating fermented foods on a regular basis, if you tolerate them, is a great way to sneak in some probiotics to support your healthy gut bacteria. But it may not be enough to recover the damage from antibiotics. For this reason, I recommend adding a quality probiotic supplement.

The Bottom Line

Taking probiotics with antibiotics isn’t just safe, it’s one of the most effective ways we know of to protect your gut health, reduce common side effects like diarrhea, and support a quicker recovery. While outdated concerns about timing and strain specificity still circulate, the research overwhelmingly supports using high-quality, multi-strain probiotics alongside antibiotic therapy.

Whether you’re currently on antibiotics or preparing for a course, now is the time to take control of your gut health. Take a proactive approach and download our free Gut Reset Guide to get practical, step-by-step strategies for restoring balance, reducing digestive symptoms, and choosing the right probiotics for your body.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.