Fact checked by Nick Blackmer

• Digestive issues like bloating and acid reflux are common during perimenopause.
• Hormonal shifts—especially declining estrogen—likely contribute to these symptoms.
• Treatment typically targets individual digestive symptoms, rather than relying on hormone therapy.

Digestive issues like bloating, acid reflux, and changes in bowel habits aren’t typically considered hallmark symptoms of perimenopause—but they’re far from rare. In fact, one recent study found that 76% of nearly 13,000 users of the period tracking app Flo who reported perimenopausal symptoms experienced digestive problems—putting them on par with more widely-recognized issues like exhaustion, mood changes, and sleep disturbances. 

Hormonal shifts during perimenopause—the transition leading up to menopause—can affect the body in ways that make people more prone to digestive problems, experts said.

Here’s what could be happening in your digestive system during perimenopause, as well as what may help bring some symptom relief.

Why Digestive Issues Are Common During Perimenopause

There’s limited research on why digestive issues tend to increase during perimenopause. The connection is “just now being looked at,” Chrisandra Shufelt, MD, associate director of the Women’s Health Research Center at Mayo Clinic in Jacksonville, Florida, previously told Health. Still, there are a few theories.

One key factor is thought to be the two-way relationship between the gut microbiome—the community of microbes living in the digestive tract—and the sex hormones estrogen and progesterone, said Lauren Streicher, MD, a clinical professor of obstetrics and gynecology at Northwestern University Feinberg School of Medicine.

During perimenopause, levels of estrogen and progesterone fluctuate unpredictably and gradually decline. The loss of these hormones, which help regulate gut health, may accelerate the natural, age-related drop in beneficial gut bacteria diversity, explained Karen E. Adams, MD, a clinical professor of obstetrics and gynecology at the Stanford University School of Medicine. At the same time, Streicher said, a less diverse microbiome isn’t as effective at regulating estrogen and progesterone.

Taken together, these effects can create a vicious cycle that Adams said leaves the gut more vulnerable to chronic inflammation, which may show up as symptoms like bloating and changes in bowel habits.

Estrogen and progesterone also influence muscle tone, including in the digestive tract. Lower levels during perimenopause may help explain why chronic acid reflux, or GERD, becomes more common during this phase, Streicher noted. GERD is typically caused by a weakened lower esophageal sphincter, the muscle that prevents stomach contents from flowing back into the esophagus.

Another possible factor is an increase in cortisol and other stress hormones during perimenopause, said Asma Khapra, MD, a board-certified gastroenterologist with Gastro Health in Virginia who specializes in women’s digestive health. Because the gut and stress system are tightly connected, higher stress levels can disrupt digestion.

Is It Perimenopause or Something Else?

While hormonal changes can trigger gastrointestinal symptoms, it’s not always clear whether they’re the cause—or if something else is going on. 

One way to suss it out is to look at the age of the patient—perimenopause generally hits during the 40s or 50s—and whether they’re experiencing other perimenopausal symptoms, Khapra said.

“If the GI symptoms tend to cluster with a whole host of symptoms seen in perimenopause or menopause, then we often think they are related,” she said. 

For people with existing digestive issues like reflux, bloating, and constipation, those symptoms may also worsen during perimenopause, she added.

Even so, hormonal changes shouldn’t automatically be assumed to be the cause. It’s important to rule out underlying gastrointestinal disorders, Khapra said, especially if there are red flags like bleeding, weight loss, and anemia, which may require further investigation.

What's the Treatment?

Experts stressed the importance of checking in with a healthcare provider if you think you're in perimenopause and have digestive issues—both to get treatment and to rule out other potential causes.

“If your symptoms are persistent and bothersome, you should see a gastroenterologist,” Streicher said. “Don’t just brush it off. It might be perimenopause but there could be other reasons and it’s important to make sure nothing else is going on.”

If your doctor does suspect perimenopause, Striecher said it’s unlikely that they would prescribe hormone therapy, a pill or patch containing estrogen or a mix of estrogen and progesterone. While that’s often considered the gold standard treatment for perimenopausal symptoms like hot flashes, fatigue, mood changes, and sleep issues, that’s not the case when it comes to digestive symptoms, Striecher said.

In fact, some research suggests hormone therapy may even worsen certain gastrointestinal conditions. One study found post-menopausal women taking hormone therapy were more likely to experience GERD than those who were not. 

“We can’t explain why HT has no impact or makes symptoms worse,” Streicher said, noting that ingesting or absorbing hormones might not affect the digestive system in the same way as naturally produced ones.

Instead of prescribing hormones, doctors usually focus on targeting the specific gastrointestinal symptoms themselves while keeping perimenopause in mind—for example, recommending magnesium supplements for constipation, which may also support sleep, she said.

Beyond medication or supplements, shifts in lifestyle habits may help. One of the most effective steps women can take is eating an anti-inflammatory diet that promotes gut microbiome health, Adams advised. She recommends following the Mediterranean diet, which emphasizes plant-based foods and fatty fish.

Khapra suggested aiming for 25 to 35 grams of dietary fiber per day, eating at least five different fruits and vegetables daily, and incorporating fermented foods such as yogurt or kimchi. For people dealing with constipation or bloating, she added, regular exercise can also help ease symptoms.

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