Coffee Fermentation: From Spontaneous Microbial Succession to Precision Flavor Regulation—A Comprehensive Review

The growing global demand for flavor stability and terroir expression in the specialty coffee industry has positioned postharvest fermentation as a core driver of coffee quality upgrading, second in importance only to cultivar genetic improvement. Coffee fermentation is shifting from an empirical spontaneous pectin-removal process to a precision biotechnological approach for targeted flavor regulation, with microbial communities acting as core mediators of biochemical transformation. This review compiles key research progress in coffee fermentation from 2018 to 2026, spanning processing paradigms, microbial ecology, flavor metabolic mechanisms, sensory safety, and industrial iteration. It compares the microenvironmental characteristics and microbial succession of four mainstream processing modes; clarifies functional divergence and terroir effects of the core microbiota; dissects the multi-stage cascade flavor metabolic network; and explains how fermentation precursors transfer to roasted coffee flavor. Importantly, most microbiota–flavor associations in current studies remain correlative rather than experimentally proven causal relationships. Evidence indicates that inoculated fermentation can improve cupping quality, reduce batch-to-batch variation, and mitigate biosafety risks. Several proposed precision fermentation approaches remain at the laboratory and pilot-scale stage and are not yet widely deployed industrially. Current field bottlenecks include poor regional adaptability of commercial starters, limited real-time monitoring tools, and ambiguous microbiota–flavor causal mechanisms. Future research will focus on terroir-adapted synthetic consortia, AI-driven precision fermentation, and multi-omics integrated studies, to advance coffee processing from empirical craft to precision biomanufacturing.