Can Probiotics Cause Diarrhea? What You Should Know

Overview

• Yes, some people experience temporary diarrhea when starting probiotics as their gut microbiome adjusts to the new microbes.
• This initial change is usually mild and tends to resolve within a few days to a couple of weeks of consistent daily use.
• Diarrhea during this phase is typically due to shifts in microbial populations and increased bacterial activity, not a harmful “die-off” reaction.
• Factors like the specific probiotic strains, the dosage, added prebiotics, and your individual gut sensitivity can influence whether you experience diarrhea.
• While temporary adjustments are common, consult your healthcare provider if diarrhea is severe, contains blood, is accompanied by fever, or persists beyond a few weeks.

So, you’ve decided to support your gut health by adding probiotics to your routine. (Woohoo! 🎉) You’re probably anticipating benefits like smoother digestion or maybe even support for your skin or heart health. But instead of immediate relief, you find yourself sprinting to the bathroom more than you’d like. And this probably made you wonder, “Wait… can probiotics cause diarrhea?”

If you’re experiencing loose stools after starting probiotics, you’re not alone! It’s one of the potential, albeit temporary, side effects some people notice. The good news is that it’s often a sign that things are shifting internally—your gut microbiome is reacting to its new arrivals. 

But why does this happen, how long does it last, and what can you do about it? Let’s explore the science behind this.

Why Do Probiotics Sometimes Cause Temporary Diarrhea?

Introducing billions of live microorganisms into your gut is like throwing a (hopefully friendly) party in an apartment that’s already at capacity. Sometimes, the initial integration causes a bit of temporary commotion, which can manifest as changes in your poop habits, including diarrhea. 

Here’s a breakdown of the potential reasons why probiotics may cause loose stools:

Microbial Shifts: Adjusting to Your New Microbes

Your gut is home to trillions of microbes, living in a complex and established ecosystem.¹ When you introduce new probiotic strains, even beneficial ones, it can cause temporary shifts in the balance of your existing microbial community. This period of flux, as your resident microbes and the newcomers get acquainted, can sometimes alter gut function and lead to looser stools as your system adapts.^2,3

Think of it as your internal ecosystem finding a new equilibrium.

Increased Microbial Activity and Fermentation

Probiotics are living microorganisms, and when they arrive in your gut—specifically the colon—they become metabolically active. Many probiotic bacteria, along with your resident gut microbes, ferment fibers and other prebiotics (specialized compounds that are used by beneficial bacteria as an energy source.)⁴

This microbial fermentation process produces valuable compounds like short-chain fatty acids (SCFAs), but it also creates gas (like hydrogen, methane, and carbon dioxide) as a byproduct.⁵ (Raise your hand if your probiotics also make you fart more! 🙋)

A sudden increase in fermentation activity can lead to temporary gas, bloating, and sometimes changes in stool consistency. This includes diarrhea, particularly if your diet is high in fermentable fibers or if the probiotic itself contains prebiotics. ⁶ 

💊 Probiotics Fun Fact! When a probiotic also contains prebiotics, it’s called a synbiotic.

Changes in Gut Motility

The SCFAs produced during fermentation don’t just feed your colon cells; they can also influence gut motility—the muscular contractions that move food and waste through your digestive tract.^7,8 Some SCFAs can stimulate these contractions. 

While this can be helpful for relieving constipation, a sudden increase in contractions and movement may temporarily lead to faster transit times. In other words, you may notice that your poop travels through your system a bit more quickly than you’re used to. As a result, some people may experience looser stools as their gut adjusts to this new level of microbial activity.⁹

Is Diarrhea a Sign Probiotics Are Working?

It’s understandable to feel concerned if you start taking something for your health and end up feeling worse at first. You may even wonder if this new diarrhea means that your probiotics are “too strong” for you, or if your probiotics are even working. These are valid concerns. But let’s learn more about this before we sound the alarm.

Ever heard of “die-off” reactions (also called Herxheimer reactions)? It’s sometimes used to explain symptoms like diarrhea when starting probiotics. The theory suggests that probiotics rapidly kill harmful bacteria, releasing toxins that cause unpleasant symptoms. But this concept is largely scientifically unsubstantiated in the context of probiotics.

Herxheimer reactions typically happen in very specific scenarios, like certain bacterial infections or antibiotic treatments—not from taking probiotics.¹⁰ Most common probiotic bacteria genera, such as Lactobacillus and Bifidobacterium, aren’t spirochetes—and by definition, probiotic strains must confer a health benefit to the host.11

It’s a common misconception that digestive changes like diarrhea result from a “die-off” of harmful bacteria. According to Dirk Gevers, Ph.D., Seed’s Chief Scientific Officer, these temporary symptoms are better understood as part of your gut ecosystem’s natural acclimation process. Instead of a dramatic bacterial battle, your gut is simply adapting to new beneficial microbes and their metabolic activity.¹²

Gut Reactions Are Normal

Probiotics are generally transient visitors; they interact with your resident microbes and intestinal cells as they pass through, rather than aggressively colonizing and displacing existing bacteria.¹² Temporary diarrhea usually means your gut is adapting to these interactions and the metabolic byproducts. So, while potentially uncomfortable, it’s often a sign of physiological activity and adaptation, not necessarily failure or harm. 

How Long Does Diarrhea From Probiotics Usually Last?

If you are experiencing diarrhea after starting probiotics, you’re probably wondering how long you need to endure the extra bathroom visits. For most people, this acclimation phase is short-lived.

Mild diarrhea, bloating, or gas typically subsides within a few days to a few weeks of consistent daily use.² As your gut microbiome adapts to the new probiotic strains and establishes a new balance, these initial digestive responses usually fade.

Several factors can influence how long this adjustment period lasts:

• Strains and Dose: Different strains have different effects, and higher doses might elicit a stronger initial response.^13,14
• Personal Gut Microbiome: Everyone’s starting gut ecosystem is unique. Someone with a more sensitive gut or existing microbial imbalance might take longer to adjust.¹² 
• Consistency: Taking your probiotics daily allows your gut to adapt more steadily. Skipping days can prolong the adjustment phase.
• Diet: A diet very high in fermentable fibers might contribute to more pronounced initial effects when combined with new probiotics.⁴

📲 If diarrhea lasts more than a few weeks or feels severe, check in with your doctor.

Do All Probiotics Cause Diarrhea?

Not every probiotic impacts your gut the same way—some may cause temporary diarrhea more than others. 

It all depends on a few important details:

• Strain Specificity: Different probiotic strains have unique “personalities” and jobs in your gut. For instance, S. boulardii CNCM I-745 (which is actually a yeast) and L. rhamnosus GG have been studied because they might help ease specific types of diarrhea.^15,16 Others may initially shake things up a bit more, leading to temporarily looser stools as your gut adjusts. 💡 Pro Tip: Choose probiotics that clearly identify their strains!
• Dosage (AFU/CFU Count): More isn’t always merrier. Starting with an extra-high dose might trigger a stronger initial reaction in your gut, so it’s best to choose probiotics that match the studied dosages.¹³
• Prebiotics: Some probiotics include prebiotics, and highly fermentable ones (like inulin, FOS, or GOS) might cause diarrhea at first—especially if introduced quickly or in large amounts.
• Formulation and Quality: What’s inside of a probiotic doesn’t matter if it never reaches your gut. Capsules designed to protect probiotics from harsh stomach acids and deliver them safely to your colon can make a big difference. Ultimately, the quality and careful formulation of your probiotic can greatly influence how smoothly your gut adjusts. 

How to Manage Diarrhea Caused by Probiotics

Experiencing diarrhea isn’t exactly enjoyable, especially when you’re trying to improve your gut health. If your symptoms seem mild and related to starting probiotics, there are ways to manage it.

Strategies to get you through:

1. Stay Hydrated: Diarrhea means watery stools—and that fluid has to be replenished somehow. Drink plenty of water or electrolyte-containing beverages to keep your body hydrated. (Your gut loves water almost as much as it loves microbes. 😍)¹⁷
2. Be Patient (If It’s Mild): We get it, patience isn’t always easy—but your gut appreciates it. Mild diarrhea when starting probiotics is typically short-lived. Sticking with your routine for a week or two could allow your system to settle into a new normal.
3. Temporary Dose Adjustment: If the recommended dosage feels too intense, consider temporarily reducing your intake (like taking one capsule instead of two.) Once symptoms ease, gradually return to the full dose. It’s like easing into a new workout—you wouldn’t sprint full-speed on your first run, right? 🥵
4. Try with Food: Some probiotics are recommended on an empty stomach, but taking them alongside a meal can help soften digestive changes for some people. (Probiotics are happy to join you at mealtime—no complaints here!)¹⁸

But, then again, It’s also possible that the diarrhea you’re experiencing might not even be related to probiotics at all.^19,20,21

Important: If symptoms become severe, include blood or mucus, or come with fever or vomiting, don’t hesitate—contact your healthcare provider right away. (They’d much rather you call sooner than later.) Also, if diarrhea continues for more than two or three weeks, especially if you have existing health conditions or a weakened immune system, it’s important to check in with your doctor.²²

Other Reasons You Might Have Diarrhea

Consider other potential causes like:

• A stomach bug or food poisoning 🤢
• Eating something your body doesn’t agree with (like an intolerance)
• Starting new medications or supplements
• Another underlying digestive factor

Your healthcare provider can help pinpoint the exact cause and guide you on the best next steps.

The Key Insight

Experiencing diarrhea after starting probiotics might seem counterintuitive—but it’s usually just your gut adjusting to new microbial visitors. This temporary phase is known as the adjustment period, and it’s a normal part of integrating probiotics into your routine. Staying hydrated, adjusting your probiotic intake if needed, and giving your gut a bit of patience usually helps ease this transition. 

🌱 Good things take time—your gut’s adaptation included. Keep cultivating. 

Frequently Asked Questions (FAQs)

Do I Need to Stop Probiotics If I Get Diarrhea?

Not necessarily—mild diarrhea can be a normal part of your gut adjusting. Lower the dose, try taking them with food, and hydrate. If symptoms get severe or prolonged, chat with your healthcare provider.²³

How Long Does Diarrhea Last After Starting Probiotics?

Typically, probiotic-related diarrhea eases within a few days to two weeks as your gut adjusts to the new microbes.² If it lasts longer than that or feels severe, it’s a good idea to talk with your healthcare provider.

Can Probiotics Make Diarrhea Worse?

It’s possible. Some people notice their diarrhea temporarily worsens at first. However, certain strains, like S. boulardii CNCM I-745 and L. rhamnosus GG, are specifically studied because they might actually help manage occasional diarrhea.^15,16 

If you’re already experiencing diarrhea, talk to your doctor before adding probiotics to your routine.

How Do I Know If My Probiotics Are Working?

Everyone is different! Once your gut adjusts, you might notice steadier digestion, less gas and bloating, and more comfortable poops. Some probiotic strains may also offer additional benefits, like clearer skin or immune support.^15,24 

✨ Remember, probiotic effects depend on the strains you choose and consistent daily use.