The impacts of climate change on coffee trees are hard to foresee and dependent on the cropping system (ranging from high input monocultures to almost natural agroforestry associations), soil and water resources. Pests and diseases are also affected. Research on adaptation to climate change is mainly focused on cereals but there are few studies on perennial tropical crops where stress can alter the behaviour of the plant for several seasons. Some parasites can adapt more quickly to climate change than the perennial host plants and spread into new habitats. The aim of CIRAD's coffee genetic improvement research is to obtain 'healthy' crops, i.e. more resilient and resistant. Here we present integrative approaches focused on the functioning of the genome (transcriptomic, metabolomic, genomic, epigenetic) and the whole plant, as well as adaptive responses to combined stresses. The goal is to propose targets for coffee breeding in order to improve resistance to coffee rust, nematode control and adaptation to drought.