Besides genotypic characteristics, the crucial factor that determines coffee quality is the mode of post-harvest treatment, i.e., the wet and dry processing. Up to now, the resulting characteristic flavour differences between these differentially processed coffees were attributed exclusively to differences in starting material. However, as these quality differences are still evident, even when identical coffee samples were processed by the two methods in parallel, the differences must be created by metabolic processes in the coffee beans themselves. Based on expression studies of the germination-specific isocitrate lyase and the resumption of cell cycle activity, monitored by the abundance of beta-tubulin, we evidence that germination is initiated in coffee seeds during the course of standard coffee post-harvest treatments. The extent and nature of the germination processes depend on the processing method. The coherence of metabolic events, substantial differences in the chemical composition of the coffee beans, and the generation of specific coffee qualities establishes the basis for a quite novel approach in coffee research.