Fruit trees, as perennial plants, continuously face the threat of various pests and diseases, making disease resilience essential for their survival and productivity. We define resilience as the tree ability to sustain itself or quickly recover after exposure to pathogens, aiming to design ‘resilient ideotypes’ that can maintain growth and productivity despite environmental pressures. This study proposes to evaluate disease resilience in a 206 individual peach core-collection by measuring so-called resilience biomarkers, including trunk growth, flower density, and fruit load. These measurements were conducted alongside visual assessments of 7 pest and disease symptoms in low phytosanitary conditions at three locations in southeastern France during three consecutive seasons. From this large dataset, we developed a multi-disease index and a four-category resilience classification to identify peach varieties that can withstand multiple biotic stresses. Finally, we compared i) multivariate GWAS model, ii) index based GWAS and iii) PCA based multi-trait genome-wide association studies (GWAS).Our findings demonstrated the effectiveness of these biomarkers in defining resilient varieties tailored to their specific environments. Sixteen co-localizing peaks were identified, suggesting possible pleiotropic effects of genes that influence immunity against multiple pests, diseases, and resilience indices. As a result, this study offers initial insights into the genetic structure of disease resilience components in peach.By prioritizing resilience in breeding programs, we aim to develop more sustainable orchards via the use of varieties that can resist diseases while minimizing the use of pesticides.