The present review represents a recent state of the art of the consequences of drinking coffee at the different levels of the gastrointestinal tract. At some steps of the digestive process, the effects of coffee consumption seem rather clear. This is the case for the stimulation of gastric acid secretion, and of biliary and pancreatic secretion, the reduction of gallstone risk, the stimulation of colonic motility, and changes in the composition of gut microbiota. Other aspects are still controversial, such as the possibility for coffee to affect gastro-esophageal reflux, peptic ulcers, and intestinal inflammatory diseases. This review reports the available evidence on different aspects of digestion and identifies the areas that would most benefit from additional studies.