Modern breeding for fruit plants require bioinformatics support to store and rationalize the abundance of available phenotypic and genotypic data. Critical requirements are standardization and database interoperability, necessary to avoid the creation of “data islands” that won’t serve beyond the specific scope of the project (or task) that generated it. It is moreover necessary to intensify the connection between scientific genetics research and application to breeding. The FruitBreedomics project aims specifically to connect academia and breeders, with focus on apple and peach, two of the most important fruit crops in Europe and in the world. We here present a bioinformatics facility that has been designed for long term storage and fruition of all the data produced and collected during the project. The design choices focused on (re)use of available database schema and data harmonization. The database currently stores almost a million single phenotypic entries covering 111 traits linked to fruit quality and fruit yield. Three types of genetic data (SSR, SNP array datasets, and haplotype blocks) are stored, together with information about more than 13 thousands trees. The infrastructure contains also ad hoc “push