This study delivers the first comprehensive proteomic characterization of the insect vector Euscelidius variegatus following the acquisition of Flavescence dorée phytoplasma. Flavescence Dorée (FD) is a quarantine disease that leads to severe vine decline and yield reduction in vineyards across Europe. By integrating newly generated genomic resources with advanced data-dependent acquisition (DDA) and data-independent acquisition (DIA) mass spectrometry data, we systematically investigated the intricate molecular interactions underpinning the tripartite relationship among the insect host, its microbiome, and the phytoplasma pathogen.