Dataset collected from dendroecological study on trunks of grapevines ('Chardonnay' cv.) infected by the "Flavescence dorée" phytoplasma (FDp) in Origlio (southern Switzerland) in 2019-2020. Ring widths were measured with cellSens (Olympus Corporation). Calculations and analysis were conducted within R. The Flavescence dorée phytoplasma (FDp) causes a severe grapevine (Vitis vinifera) disease. Anatomical modification due to FDp infections are known to occur but research so far focused on stems and leaf tissues and, in particular, on their phloem structure. In this paper, we applied dendrochronological techniques on wood rings and analysed the anatomical structures of the trunk of the susceptible grapevine cultivar ‘Chardonnay’ in order to verify their response to FDp infections. In this study, we tested the impact of FDp and drought stress on xylem ring width and also described phloem anomalies inside the trunk of grapevines. We concluded that drought and FDp infection both have a significant effect on ring width reductions and that FDp supersedes the effect of drought conditions (calculated after the SPEI index) in infected specimens.