As perennial plants, fruit trees must cope, individually, with the fluctuating threat of multiple pathogens over the years. In this long-lasting battle for plant immunity, disease resilience is emerging as a key mechanism for tree survival and fitness. More fundamental research is required to improve our understanding of disease resilience mechanisms, which in turn could be particularly relevant for a more sustainable fruit production. As this approach is novel for that field, we propose i) a clear definition of resilience for fruit producing trees, ii) a methodology for studying its phenotypic components which requires repeated measures of “resilience biomarkers”, iii) to decipher the genetic architecture of resilience components, and iv) an innovative strategy based on high-throughput phenotyping and genomics for identifying resilient genotypes. All in all, disease resilience appears as a meaningful breeding perspective in a context of unprecedented plant protection restrictions.