Reserve compounds that accumulate in coffee seeds contribute to a large extent– directly or through roasting-induced chemical reactions – to the broad spectrum of aromas and flavours of the coffee cup. Coffee seed reserves are mainly composed of cell wall polysaccharides, lipids, proteins, sucrose and secondary metabolites including chlorogenic acids, caffeine and trigonelline. Understanding coffee quality requires a detailed characterization of the metabolic pathways dedicated to the synthesis of these aroma/flavour precursors. This chapter describes the current state of knowledge on the relationships between coffee quality, seed chemical composition, and genetic and environmental effects, with a special focus on environmental regulations of coffee seed metabolic pathways. It includes a case study on coffee production on La Réunion Island and provides suggestions for further reading as well as looking ahead to future developments in coffee seed chemical composition research.