5 Possible Reasons Why Gut-Friendly Foods Make Your Stomach Feel Like Garbage (2024)

Yes, yes, we get it: Gut health is essential for overall health, and feeding your gut foods that promote digestive health—probiotics, prebiotics, fermented foods, and fiber—is an important part of healthy eating. So why is it that I feel like a bloated, burpy monster after a bottle of kombucha or a serving of kimchi?

Of course, this isn't the case for everyone. Otherwise, why would people recommend eating them in the first place? But for some people (myself included), certain "gut-friendly" foods can sometimes feel anything but. I talked to two registered dietitians to get to the bottom of why that can happen, and how to deal with it.

1. You might be going all-in too quickly

“While fermented foods are great for gut health, too much too soon can definitely upset your digestive system," says Sam Presicci, MCN, RD, LD, CPT, a registered dietitian based in Texas. "For someone new to fermented, probiotic-rich foods, I always recommend they start slow, having less than the recommended serving and working their way up."

For sauerkraut, for instance, you might start with one tablespoon to get used to it—treat it like a condiment rather than dunking it on or eating with a fork. If you want to try kombucha, she suggests starting with half a bottle per day and see how you feel. Your system needs to get used to new ingredients and you need to be able to pinpoint what might be upsetting your stomach.

2. You're eating too much fiber

The average person should be getting about 25 to 29 grams of fiber per day to enjoy the nutrient's gut-boosting benefits. Eating too much fiber (especially when you're not used to it) can lead to bloating, gas, and other...ahem, fun side effects. Thankfully, the consequences of upping your intake too quickly can largely be mitigated by drinking lots of water.

It's also important to keep an eye on your prebiotic intake, as they're another form of fiber, says Amy Shapiro, MS, RD, CDN and founder ofReal Nutrition. "This is the fiber component which helps the bacteria to thrive and stay alive in the gut," she says, and they're often found in probiotic-rich foods. They're a helpful nutrient, yet they don't get digested by the body, which in excess can cause discomfort in some. “Certain yogurts contain probiotics but also contain prebiotics such as inulin, which can cause stomach upset as the body doesn’t digest this ingredient,” says Shapiro.

3. You're mixing the wrong foods

How (and when) you eat your gut-friendly foods can actually affect how it makes you feel. When we pair a gut-friendly food with a protein, for example, digestion slows (since protein takes longer to digest) and this can lead to gas and bloating, says Shapiro.

Timing and pairings matter. Many probiotic supplements should be eaten with food or right before a meal to ensure they survive your stomach's harsh acidic environment. “When it comes to high-fiber foods like cabbage and kraut, I would eat them with a salad and mostly plant-based foods in the beginning to allow for quicker digestion,” says Shapiro. Then follow it with your protein.

4. You may have a food intolerance

If you can’t handle kefir or kimchi well, you might have a food intolerance that’s unrelated to their probiotic powers. “In general, the tolerance of different fermented foods, including fermented veggies, sauerkraut, kimchi, kefir, kombucha, really varies depending on the individual,” says Presicci.

“Signs that you’re not tolerating fermented foods can range from bloating, diarrhea or constipation to skin issues, nausea, headaches and more after eating them,” she says. Each reaction will depend on the reason behind the intolerance, though, and if you do see something off consistently, it’s worth seeing a doctor for an allergy test and discussion.

Histamine intolerance is possible, since fermented foods are generally high in histamine (a compound important for the immune response). “Histamine intolerance can be caused by a genetic mutation or by an imbalance in a person’s gut flora,” says Presicci. This is pretty rare though—it's estimated about 1 percent of people have it. If you get migraines and headaches often after consuming aged cheeses, wine, chocolate, dried fruit, booze, and other triggers that have higher histamine content, and you’re not tolerating fermented foods either, it could point to a histamine issue.

5. You might be sensitive to FODMAPs

FODMAPS, which refers to a group of short-chain carbohydrates including fructose and lactose, are found in certain foods that can lead to poor digestion and irriation in some people. Some probiotic foods, like kombucha, happen to have these FODMAPs, says Shapiro. Kimchi and sauerkraut are part of this family of FODMAP foods, too, as they are cruciferous vegetables and many people have a hard time breaking down their carbohydrate chains, she adds. There are some at-home tests for FODMAP sensitivities, but it's usually best to talk to a doctor for more nuanced support and testing.

Okay, what do I do now?

“If you’re new to fermented foods, make sure to start slow in order to help avoid symptoms. But if you’re having regular negative symptoms, even after consuming small amounts of fermented foods, it’s important to figure out the underlying cause,” says Pressici. If this sounds like you, it's a good idea to pay a visit to a functional medicine doctor for testing and consultation. From there, you need to work closely with your practitioner to manage symptoms and repair your gut, and then start slowly rebuilding your gut flora. Hopefully the bloaty feeling you get with kombucha will be a thing of the past.