Berry fruits consumption has increased dramatically over the last decade due to its remarkable flavor and well-known health benefits. The demand for high-quality berry fruits and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Nowadays, to improve fruits sensorial and nutritive characteristics as well as enhanced fruit quality traits and climate change adaptation are the main objectives of breeding programs. Our aim is the identification of metabolic biomarkers associated with climate change, involved in fruit quality by using metabolomic tools. In addition, multivariate statistical analyses were applied to outline the genetic and environmental factors controlling the accumulation of quality-related metabolites, both for the organoleptic and nutritional characteristics of this highly appreciated fruit. To better understand how environment influence fruit metabolome, we study the metabolomic profiles of mature fruit from four raspberry and black currant commercial cultivars grown in different European locations (Germany, Poland, Norway and Scotland). Our result suggests that environment has a strong impact on primary metabolites and volatiles, such us increase in β-ionone due to high radiation in raspberry fruit or vitamin C accumulation according to differences between day and night temperatures in black currant fruits. Besides, both cultivars appear to be better adapted to North Europe growing conditions, for example they favor the accumulation of SSC and organic acids. Further, we corroborate the impact of environmental factors have on fruit flavor and nutritional value and how metabolomic approaches are suitable for assessing fruit quality.