What happens to your body when you suddenly stop drinking coffee? To find out, researchers from University College Cork in Ireland studied 62 people, half of whom regularly drank three to five cups of coffee a day and the other half who didn’t usually drink coffee. They examined gut bacteria, metabolites, mood, stress, alertness, learning and memory.
Regular coffee drinkers first stopped drinking coffee for two weeks, during which time the researchers measured changes in their bodies and behavior. Coffee was then reintroduced, but participants did not know whether they were drinking a caffeinated or decaffeinated beverage.
The most obvious changes observed after stopping drinking coffee are in the gut. Coffee drinkers had large changes in their gut metabolites (small chemicals produced or altered by metabolism) compared to people who didn’t normally drink coffee.
When coffee was reintroduced, both the caffeinated and decaffeinated groups reported less perceived stress, lower depression scores, and lower impulsivity. Since these changes occur with both types of coffee, the effects are not necessarily dependent on caffeine.
Researchers also found some differences in the gut bacteria of coffee drinkers. Bacteria – e.g. Eggellathought to aid acid secretion in the stomach and intestines, or Cryptobacter kruseimay be involved in the production of bile acids – more abundant in coffee drinkers than in non-coffee drinkers.
Both processes may create an intestinal environment that blocks some harmful bacteria and infections.
Coffee drinkers also had higher levels of Firmicutes bacteria, a microorganism that has previously been linked to positive emotions in women.
Dr. Kelly Brown, Geviti’s medical director and a board-certified family medicine physician who was not involved in the study, told CNN newsweek Several biological pathways may help explain the link between coffee, gut health and mental health.
“The gut and brain communicate through multiple pathways, including the nervous system, immune signaling, inflammation and metabolites produced by gut bacteria,” she said. “Coffee contains compounds that can be metabolized by our gut microbes and may affect that environment.”
She added that these changes may affect inflammation, neurotransmitter signaling and other pathways involved in mood, stress and cognition.
“But we’re still studying the importance of each mechanism,” Brown continued.
One major difference was observed between caffeinated and decaffeinated coffee.
Improvements in learning and memory were seen in people who drank decaffeinated coffee, but this was not observed in the caffeinated group. This means caffeine may not account for all of the effects coffee may have on cognition.
The researchers pointed to other compounds in coffee, including polyphenols, as possible causes.
Brown noted that polyphenols, specifically chlorogenic acid, are among the most important non-caffeine compounds in coffee.
“They have antioxidant and anti-inflammatory properties and can also be metabolized by gut microbes into other bioactive compounds. Coffee also contains soluble fiber and other plant compounds that can interact with gut bacteria, so coffee’s effects are much more complex than caffeine alone,” she said.
Meanwhile, caffeinated coffee can reduce anxiety, increase alertness and focus, and reduce the risk of inflammation.
Professor John Cryan, principal investigator of the APC Microbiome at University College Cork in Ireland and corresponding author of the study, said in a press release: “The public’s interest in gut health has greatly increased. The relationship between digestion and mental health is increasingly better understood, but the mechanism behind the impact of coffee on the gut-brain axis remains unclear.
“Our findings shed light on how the microbiome and coffee respond to the nervous system and their potential long-term benefits for a healthier microbiome. Coffee may alter the collective behavior of microbes and the metabolites they use.
“As the public continues to consider dietary changes to achieve the right digestive balance, coffee has the potential to be used as a further intervention as part of a healthy balanced diet.”
Klein adds that coffee is more than just caffeine. “It’s a complex dietary factor that interacts with our gut microbes, metabolism, and even emotional health,” he said.
Brown cautioned that the findings should be interpreted carefully.
“Association does not necessarily mean causation,” she said, noting that coffee drinkers may differ in how much coffee they drink, the type they drink and how their bodies process caffeine.
Individual microbiomes can also vary widely, she added, and researchers should not automatically label changes in a single bacterial species as beneficial or harmful.
“The research is promising, but coffee doesn’t treat poor gut health, depression or cognitive decline,” Brown said.
refer to
Boscaini, S., Bastiaanssen, TFS, Moloney, GM, et al. (2026). Habitual coffee consumption shapes the gut microbiome and alters host physiology and cognition. Nature Communications, 17. https://doi.org/10.1038/s41467-026-71264-8
Please contact Newsweek editors Kara Dolman and Shakeema Edwards about this story.