Coffee may do more than keep you going: It could have a noticeable impact on your digestive health, even if you drink decaf.

Researchers from APC Microbiome Ireland found that habitual coffee consumption alters the trillions of microbes living in the digestive tract, creating a chemical feedback loop that directly influences mood, stress levels and cognitive sharpness.

The study followed 62 participants to determine how coffee interacts with the microbiome.

The group included 31 coffee drinkers and 31 non-coffee drinkers who went through a series of psychological tests and kept detailed journals about their diet and coffee consumption.

The researchers defined “coffee drinkers” as those consuming three to five cups daily, a range the European Food Safety Authority deems safe and moderate.

After people stopped drinking coffee for two weeks and then started drinking it again, the bacteria in their digestive systems behaved differently than the non-drinkers, according to a press release.

“Coffee is more than just caffeine,” study author John Cryan, principal investigator at APC Microbiome Ireland, said in a statement.

“It’s a complex dietary factor that interacts with our gut microbes, our metabolism and even our emotional well-being.”

The coffee drinkers were found to have higher levels of specific beneficial bacteria, such as Eggertella and Cryptobacterium curtum.

These microbes play a vital role in releasing gastric acids and creating bile, both of which help the body eliminate harmful bacteria and manage inflammation, the researchers noted.

Both caffeinated and decaf drinkers reported lower levels of perceived stress, depression and impulsivity. This suggests that the non-caffeine components of coffee, like polyphenols and antioxidants, are doing the heavy lifting for mental health.

However, the two types of brew offer different perks. Caffeinated coffee was specifically linked to reduced anxiety and better focus, while decaf was shown to lead to significant improvements in learning and episodic memory.

Researchers believe these cognitive gains in decaf drinkers may be tied to better sleep quality and increased physical activity.

The study’s findings are limited by a small sample size, which may not accurately represent the diverse microbiome profiles found across different global populations.

Because the research relied heavily on self-reported data regarding participants’ coffee habits and mood levels, the results are subject to memory errors and subjective bias, the researchers noted.

The study also did not strictly control for other dietary variables, such as sugar and dairy additives, which could independently influence gut health and cloud the specific impact of the coffee bean itself.

The research was published in the journal Nature Communications.