Abstract: Fermentation serves as a critical process in coffee fruit processing for flavor development. Microbial metabolites produced during this biochemical transformation substantially contribute to the aromatic profile and flavor characteristics of roasted coffee beans. Microorganisms degrade coffee fruit mucilage and produce metabolites such as esters, ketones, alcohols, acids, and aldehydes. The interactions between these compounds contribute to the complexity of the final flavor profile of coffee. This review systematically summarizes the predominant microbial community structures and succession of coffee fermentation processes (wet, dry, and semi-dry methods), elucidates the impacts of lactic acid bacteria, yeasts, other bacterial, and filamentous fungi on flavor development, and the underlying metabolic pathways involved in these biochemical interactions. This review aims to establish a theoretical framework for targeted flavor modulation in coffee and to advance the sustainable efficiency of coffee industry practices.