Flavescence dorée is an economically important vector-borne disease of grapevine in Europe caused by phytoplasmas belonging to the 16SrV ribosomal group. Expression profiles of 11 genes of the Flavescence dorée phytoplasma (FDp) were analysed over time following infection of natural (Vitis vinifera and the leafhopper vector Scaphoideus titanus) and experimental (Vicia faba and Euscelidius variegatus) hosts. Infected and symptomatic grapevine plants (Chardonnay) were sampled under natural field conditions in a productive vineyard in north-western Italy. Broad bean samples were assayed after the experimental inoculation with infectious E. variegatus. Adults of both vector species were analyzed following FDp acquisition from infected broad bean plants. The selected FDp genes were grouped according to their putative functions within different categories, namely ‘Membrane proteins’ (imp), ‘Regulative elements’ (spoVG, rpoD), ‘Protein metabolism, transport and secretion’ (tldD, ysdC, ftsY), ‘Stress response’ (comp83, osmC), ‘ABC transporters’ (CoABC) and ‘Unknown’ function (contig12, comp115). All analyzed genes were expressed in the four different host species suggesting their crucial role during the FDp infection cycle. Moreover, some of them (contig12, CoABC, comp83, and imp) might be considered essential for phytoplasma survival irrespective of the host, while comp115 seems to be required for insect infection. We showed that FDp is metabolically more active in insects than in plants, at least according to the pool of selected genes for this study, indicating that FDp behaves differently in the two hosts compared to other phytoplasma species/strains.