Reserve compounds and secondary metabolites that accumulate in mature 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 brew. Although cultivation of coffee trees under shade or at high elevation is known to favorably affect coffee quality, quantitative data describing the influence of climatic conditions on the chemical composition of the seed are still scarce. After a review of the relationships between coffee quality, seed chemical composition and environmental effects, this report will focus on the last advances in the understanding of environmental regulations of coffee seed metabolic pathways. Using multienvironment designs displaying broad climatic variations, and parallel monitoring of gene expression levels and metabolite accumulation profiles, we showed how growth conditions - such as mean air temperature - influence, in a predictable way, fatty acid, sugar and chlorogenic acid metabolisms and alter the chemical composition of the mature seed through subtle transcriptional regulations during seed development. Progress in this area could ultimately help in developing robust genomics/metabolomics fingerprints of coffee bean origin and quality, and help in assisting breeding programs dedicated to coffee quality.