Coffee, a globally consumed beverage, has gained increasing attention for its effects on metabolic health. In this review, we explore the potential mechanisms by which coffee influences metabolism through the gut microbiota. Specifically, we review the mechanisms by which coffee polyphenols and caffeine are metabolized by gut microbes into short-chain fatty acids (SCFAs) and other metabolites, which subsequently regulate glucose metabolism, lipid metabolism, inflammatory responses, and bile acid metabolism.