Stone fruit production must address an urgent societal and environmental demand for pesticide reduction in a context of unexpected epidemiological changes due to climate change. Cultivar improvement is a promising strategy to operate a sustainable transition towards low phytosanitary management. However, to date we lack cultivars bearing multiple resistances against pests and diseases and genetic resources are underused. To tackle this issue, two core collections composed by 150 apricot and 206 peach accessions have been set up. These collections have been planted respectively in two and three sites along a North-South gradient between Valence and Perpignan (France), between 2017 and 2019. These orchards are managed under low phytosanitary protection to observe the damages of pests and diseases present in natural conditions as well as phenological variables relevant as epidemiological covariates. Thus far, we have monitored three phenological traits of interest in these young orchards: blooming date, vegetative bud break and flower density. We observed a wide phenotypic diversity within the orchards, which illustrates the high genetic diversity represented in our core collections. Moreover, we observed high values of broad sense heritability (between 0.67 and 0.90) and we identified a strong effect of the environment and of genotype by environment interactions. Our results highlight the importance of a multi-site and multi-annual design to account for these effects for breeding perennials. To our knowledge, our design deployed with the objective of studying the multiple resistances to pests and diseases in apricot and peach, is the first of such amplitude. This project paves the way for future genome-wide association studies aiming at identifying candidate genes for multiple resistances to develop marker assisted selection.