Fermented Food Intolerance: 5 Signs and Symptoms
Health ConditionsDigestive Health

4 Signs Fermented Foods Don’t Agree With Your Gut

4 Signs Fermented Foods Don’t Agree With Your Gut
Getty Images
By
Updated on October 29, 2025
by

Fermented foods like kimchi, kombucha, and kefir are more than just delicious — their good bacteria can also provide gut health benefits. But for some people, fermented foods may have the opposite effect, leading to diarrhea, stomach cramping, and other uncomfortable symptoms.

To figure out whether fermented foods agree with you, Kenneth Brown, MD, a board-certified gastroenterologist in Plano, Texas, shares the top signs to look for.

Why Fermented Foods Aren’t Universally Beneficial

“Fermented foods are an excellent way to improve your gut health, as they contain beneficial bacteria that can help restore the balance of microorganisms in your digestive system,” Dr. Brown says.

Fermented foods that contain live active bacteria “have been linked to various health benefits, such as reducing symptoms of lactose intolerance, inflammatory bowel disease (IBD), Crohn’s disease and ulcerative colitis, irritable bowel syndrome (IBS), gastroenteritis, diarrhea, and even cancer,” Brown adds.

But they’re not always beneficial for everyone. For example, if you have a food sensitivity or allergy to certain fermented foods, your digestive system cannot properly break them down and absorb their essential nutrients, Brown says.

If you have lactose intolerance, for instance, eating Greek yogurt or kefir could lead to diarrhea and stomach cramping.

 Other foods high in fiber, like kimchi, may cause stomach discomfort and loose stool if you’re not used to eating fibrous foods.

3 Types of Gut-Healthy Snacks for Better Digestion

Discover 3 types of snacks that are essential for a healthy gut and better digestive function.
3 Types of Gut-Healthy Snacks for Better Digestion

Next up video playing in 10 seconds

4 Signs Your Body Can’t Handle Fermented Foods

If you suspect that fermented foods are doing more harm than good for your body, keep tabs on the following side effects the next time you eat them.

1. Gas and Bloating

Brown notes that fermented foods may produce gas while you’re digesting them. A little flatulence may not be a major warning sign — unless it leads to bloating and discomfort.

2. Stomach Pain and Cramping

Some fermented foods, like sauerkraut, can cause indigestion, stomach pain, and cramping.

 If certain fermented foods worsen your indigestion symptoms, it’s best to limit the amount you eat, or at least avoid eating them on an empty stomach, says Brown.

3. Diarrhea

The good bacteria (aka probiotics) in some fermented foods can help alleviate diarrhea. However, for some people, it can have the opposite effect.

 That’s because “the beneficial bacteria in these foods can alter the balance of microorganisms in the digestive system and lead to changes in bowel movements,” says Brown.

4. Food Intolerance or Allergies

If your skin starts to itch or develop a rash after eating fermented foods along with other GI symptoms, “this can be a sign of histamine intolerance or an allergy,” says Brown. In this case, it’s best to visit an allergist to confirm a proper diagnosis.

Bottom line: Brown recommends that people eat more fermented foods if they don’t bother them.

The Takeaway

  • Fermented foods like kimchi, kombucha, and kefir can help improve your gut microbiome and digestion, but can have the opposite effect in some people.
  • If you have lactose intolerance, eating fermented foods like Greek yogurt or sauerkraut can worsen your gut symptoms.
  • Developing diarrhea, stomach pain, and itching after eating fermented foods is a sign that they might not agree with you.
  • Reach out to your primary care doctor or a gastroenterologist to learn more about fermented foods and whether they are right for you.
EDITORIAL SOURCES
Everyday Health follows strict sourcing guidelines to ensure the accuracy of its content, outlined in our editorial policy. We use only trustworthy sources, including peer-reviewed studies, board-certified medical experts, patients with lived experience, and information from top institutions.
Resources
  1. Leeuwendaal NK et al. Fermented Foods, Health and the Gut Microbiome. Nutrients. April 6, 2022.
  2. Pyo Y et al. Probiotic Functions in Fermented Foods: Anti-Viral, Immunomodulatory, and Anti-Cancer Benefits. Foods. July 28, 2024.
  3. Malabsorption. Cleveland Clinic. April 6, 2022.
  4. Lactose Intolerance. Mayo Clinic. September 22, 2025.
  5. Krzysztof S et al. Two Faces of Fermented Foods—The Benefits and Threats of Its Consumption. Frontiers in Microbiology. March 7, 2022.
  6. Indigestion (Dyspepsia). Cleveland Clinic. March 18, 2025.
  7. Probiotics. Cleveland Clinic. October 30, 2023.
Meet Our Experts
See Our Editorial PolicyMeet Our Health Expert Network

Yuying Luo, MD

Medical Reviewer

Yuying Luo, MD, is an assistant professor of medicine at Mount Sinai West and Morningside in New York City. She aims to deliver evidence-based, patient-centered, and holistic care for her patients.

Her clinical and research focus includes patients with disorders of gut-brain interaction such as irritable bowel syndrome and functional dyspepsia; patients with lower gastrointestinal motility (constipation) disorders and defecatory and anorectal disorders (such as dyssynergic defecation); and women’s gastrointestinal health.

She graduated from Harvard with a bachelor's degree in molecular and cellular biology and received her MD from the NYU Grossman School of Medicine. She completed her residency in internal medicine at the Icahn School of Medicine at Mount Sinai, where she was also chief resident. She completed her gastroenterology fellowship at Mount Sinai Hospital and was also chief fellow.

See full bio
michele-ross-bio

Michele Ross

Author

Michele Ross is a beauty and wellness writer, content strategist, and copy editor currently based in Los Angeles. She has worked with brands including HUM Nutrition and Goldfaden MD, and has written for lifestyle publications such as Editorialist and RealSelf, among others.

See full bio
See Our Editorial PolicyMeet Our Health Expert Network