Your daily coffee may be changing the way your gut works

Many coffee drinkers are familiar with a common effect of their daily brew: it can get the digestive system moving. Now, researchers from the University of Copenhagen have found evidence that regular coffee consumption may influence not only gut bacteria but also the physiology of the digestive tract itself.

The study used a swallowable electronic capsule that traveled through participants’ digestive systems, measuring factors such as transit time, temperature, pH levels, and intestinal contractions.

Consistent with previous research, the scientists found that people who drank coffee regularly had a greater diversity of gut microorganisms than those who consumed coffee less often.

A diverse gut microbiome is generally considered a hallmark of a healthy digestive system, although the study did not determine whether coffee directly causes these changes. Perhaps the most interesting finding was that frequent coffee drinkers showed measurable differences in how their digestive systems functioned.

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Researchers found:

Lower pH levels in the small intestine, Increased contractions in the colon, and changes suggesting altered gut physiology beyond effects on bacteria alone.

“Frequent coffee consumption appears to affect the physiology of the gut itself, in other words, how the gut functions,” said lead author Francesca Bucci, a PhD student at the University of Copenhagen.

The increased intestinal contractions may be particularly important.

“Contractions in the gut can support healthy digestion, help prevent constipation and keep the intestinal muscles in good condition,” Bucci explained.

The researchers note that they cannot yet determine whether the lower intestinal pH observed in coffee drinkers is beneficial or harmful. However, pH plays a key role in digestion because it influences enzyme activity and how food is broken down.

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The study does not prove that coffee alone caused the observed differences. Still, senior author Henrik Munch Roager believes coffee is likely playing a significant role.

“We already know from other studies that coffee can influence a range of processes in the digestive system, including acid secretion in the stomach. So there are good reasons to believe that what we are seeing is not merely coincidence. Anecdotally, many people also report that coffee affects their digestion,” he said.

The researchers say the next step is a controlled intervention study where participants alternate between periods of high coffee consumption and no coffee consumption. This would help determine whether coffee directly causes the changes observed.

The findings could have practical implications for millions of people who struggle with digestive issues.

“A great many people struggle with constipation and irregular bowel movements. If we can understand how coffee affects digestion and intestinal contractions, it may be possible to use that knowledge to stimulate gut motility in a natural way,” Roager said.

Coffee has already been linked to reduced risks of cardiovascular disease, type 2 diabetes, depression, and several cancers. This study adds to growing evidence that coffee’s effects extend deep into the digestive system.

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Although additional research is required to determine whether or not there is a cause-and-effect relationship between the two, this study indicates that drinking coffee on a daily basis may not only keep you awake, but it can also alter the composition of your gut microbiome as well as how your body processes foods.

Journal Reference:

1. Francesca Bucci, Marie-Luise Puhlmann, Paula Rodriguez-Garcia et al. Habitual coffee consumption is linked to differences in gut microbiota and gut physiology. Gut Microbiology. DOI: 10.1016/j.gutmic.2026.100018