Many tropical tree crops are threatened by climate change (CC), including coffee which is highly sensitive to high temperatures, droughts and diseases. 60% of coffee today is cultivated in Agroforestry Systems (AFS), which reduce dependence on external inputs and mitigate the adverse effects of CC. So far, however, breeding has developed cultivars only for open-sun cultivation. Using new Arabica coffee F1 hybrids as a case study, we will design and test coffee varieties, better adapted to AFS and CC and maintaining a robust defense system to biotic and abiotic stresses. By doing so, we will show how breeding programs can benefit both smallholder farmers by improving their incomes, increase the options for sustainability, and benefit the European industry through sustained supplies and a wider range of specialty coffees. The project will take advantage of hybrids, established in 8 countries (Portugal, France, Nicaragua, Costa Rica, French Guyana, Cameroon, El Salvador, Vietnam) under controlled conditions (temperature, light, CO2), field trials and networks of on-farm plots. GxE will be assessed through a multidisciplinary approach where genotypes will be grown in a wide range of environments and low-input management inherent to AFS. Farmers will participate in developing the farm assessment methodology and their experiences with new hybrids (profitability, social acceptance) will inform the breeding strategy. Roasters will be involved in the breeding process through evaluation of beverage quality. By combining extensive phenotyping with metabolomic and transcriptomic analysis, we will develop analytical and predictive tools for Coffee Metabolic Networks, leading to marker aided rapid selection and a new approach for breeding of perennial crops. Impacts will be ensured by innovation platforms, technology transfer for clonal propagation, promotion of direct trading between roasters and farmers, and promotion of new hybrids adapted to AFS.