Probiotics are live bacteria and yeasts that benefit your health—particularly your gut.
You can get them from supplements or fermented foods like yogurt, kefir, sauerkraut, kimchi, and kombucha.
Research shows probiotics can improve digestion, reduce infection risk, and support overall health. But like any supplement, they can cause side effects in some people.
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Available on the App StoreThe good news: most side effects are mild and temporary. A systematic review examining probiotic safety found that while adverse effects do occur, they’re generally minor and resolve on their own.1
Here are the 5 most common probiotic side effects and how to manage them.
1. Digestive discomfort
The most frequently reported side effect is temporary digestive upset—gas, bloating, or changes in bowel habits.
Bacteria-based probiotics (like Lactobacillus and Bifidobacterium strains) may cause gas and bloating. Yeast-based probiotics (like Saccharomyces boulardii) sometimes cause constipation and increased thirst.
Why does this happen? When you introduce new bacteria to your gut, your microbiome needs time to adjust. The new organisms may produce gas as they establish themselves, and existing bacteria may be displaced.
A meta-analysis of 28 randomized controlled trials found that probiotics did not significantly increase adverse events compared to placebo in people with IBS—suggesting that while some individuals experience side effects, probiotics are generally well-tolerated.2
How to reduce it:
- Start with a low dose and gradually increase over 2–4 weeks
- Take probiotics with food
- Stay hydrated
- If symptoms persist beyond a few weeks, try a different strain or formulation
Related: Ways to reduce bloating | Foods that help with bloating
Summary: Gas and bloating are the most common probiotic side effects. They usually resolve within a few weeks as your gut adjusts.
2. Headaches from fermented foods
Probiotic-rich foods like yogurt, sauerkraut, and kimchi contain biogenic amines—compounds that form during fermentation.
Common amines include histamine, tyramine, tryptamine, and phenylethylamine. In sensitive individuals, these can trigger headaches or migraines by affecting blood flow and the nervous system.
One study found that 75% of participants with frequent headaches improved on a low-histamine diet. However, results are mixed—other research hasn’t found a strong link between dietary amines and headaches.
How to reduce it:
- Keep a food diary to identify triggers
- If fermented foods cause headaches, switch to probiotic supplements instead
- Supplements don’t contain the amines found in fermented foods
Summary: Biogenic amines in fermented foods may trigger headaches in sensitive people. Probiotic supplements are an alternative.
3. Histamine reactions
Some probiotic strains produce histamine in the gut. For most people, this isn’t a problem—the enzyme diamine oxidase (DAO) breaks down histamine before it causes symptoms.
But people with histamine intolerance produce insufficient DAO. Excess histamine gets absorbed into the bloodstream, causing symptoms like:
- Itching or hives
- Runny nose or nasal congestion
- Watery eyes
- Digestive upset
- Headaches
Histamine-producing strains include certain species of Lactobacillus buchneri, Lactobacillus helveticus, Lactobacillus hilgardii, and Streptococcus thermophilus.
How to reduce it:
- Choose strains that degrade histamine rather than produce it (such as Bifidobacterium infantis, Bifidobacterium longum, and Lactobacillus plantarum)
- Avoid high-histamine fermented foods
- Consider working with a healthcare provider if you suspect histamine intolerance
Summary: Certain probiotic strains produce histamine, which may cause allergy-like symptoms in people with histamine intolerance.
4. Reactions to other ingredients
Probiotic supplements often contain more than just bacteria. Check labels for potential allergens or problematic ingredients:
Suggested read: Food Fermentation: Benefits, Safety, Food List, and More
Common allergens:
- Dairy (milk proteins or lactose)
- Soy
- Egg
- Gluten
Lactose: Many probiotics contain small amounts of lactose as a carrier. While most people with lactose intolerance tolerate up to 400 mg in supplements, some may experience gas or bloating. Look for lactose-free options if needed.
Prebiotics: Some supplements combine probiotics with prebiotic fibers (inulin, FOS, or lactulose) and are called synbiotics. Prebiotics feed beneficial bacteria but can cause gas and bloating in some people—especially those with IBS.
Yeast: Yeast-based probiotics like Saccharomyces boulardii should be avoided by people with yeast allergies.
Summary: Read labels carefully. Probiotics may contain allergens, lactose, or prebiotic fibers that cause reactions in sensitive individuals.
Related: Probiotics and prebiotics
5. Infection risk in vulnerable populations
For healthy people, probiotics are extremely safe. But in rare cases, the bacteria or yeast can enter the bloodstream and cause infection.
A comprehensive systematic review identified the groups at risk:1
- People with suppressed immune systems
- Critically ill patients in ICUs
- Those with central venous catheters
- Post-surgical patients
- People with severe acute pancreatitis
The risk is very low. Estimates suggest about 1 in 1 million people taking Lactobacillus-based probiotics develop an infection. For yeast-based probiotics, it’s about 1 in 5.6 million.
A meta-analysis of 80 randomized trials in people with autoimmune and rheumatic diseases found that probiotics did not significantly increase adverse events compared to placebo.3
When to be cautious: If you fall into any high-risk category, talk to your doctor before starting probiotics. The benefits may still outweigh the risks, but medical supervision is important.
Summary: Probiotics can rarely cause infections in severely immunocompromised individuals. Healthy people face minimal risk.
How to minimize probiotic side effects
Most side effects are preventable or manageable:
Suggested read: Should You Take Probiotics During Pregnancy? Benefits & Safety
Start low, go slow. Begin with a lower dose than recommended and increase gradually over 2–4 weeks.
Take with food. This buffers stomach acid and helps bacteria survive to reach the intestines.
Stay hydrated. Water helps fiber move through your system and may reduce bloating.
Give it time. Most digestive side effects resolve within 2–3 weeks as your gut microbiome adjusts.
Try different strains. If one probiotic doesn’t agree with you, another might. Strains have different effects.
Read labels. Avoid ingredients you’re sensitive to—allergens, lactose, prebiotics, or specific strains.
Related: Best time to take probiotics | Ways to improve gut bacteria
When to stop taking probiotics
Discontinue use and consult a healthcare provider if you experience:
- Severe abdominal pain
- Symptoms that worsen rather than improve after 3–4 weeks
- Signs of allergic reaction (hives, swelling, difficulty breathing)
- Fever or signs of infection
These reactions are uncommon but warrant medical attention.
Bottom line
Probiotics are safe for most people. The most common side effects—gas, bloating, and digestive changes—are usually mild and temporary.
People with histamine intolerance, food allergies, or compromised immune systems should choose probiotics carefully and may benefit from medical guidance.
If you experience side effects, try starting with a lower dose, switching strains, or opting for supplements instead of fermented foods. Give your gut 2–3 weeks to adjust before deciding whether probiotics work for you.
Related: Probiotics for constipation | Probiotics and weight loss
Didari T, Solki S, Mozaffari S, Nikfar S, Abdollahi M. A systematic review of the safety of probiotics. Expert Opin Drug Saf. 2014;13(2):227-239. PubMed ↩︎ ↩︎
Sun JR, Kong CF, Qu XK, et al. Efficacy and safety of probiotics in irritable bowel syndrome: A systematic review and meta-analysis. Saudi J Gastroenterol. 2020;26(2):66-77. PubMed ↩︎
Zeng L, Yang K, He Q, et al. Efficacy and safety of gut microbiota-based therapies in autoimmune and rheumatic diseases: a systematic review and meta-analysis of 80 randomized controlled trials. BMC Med. 2024;22(1):110. PubMed ↩︎
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