Here we investigate the effect of agricultural integrated management on soil microbial diversity within a vineyard with a history (20 years) of exposure to frequent applications of fertilizers and pesticides each season. Considering that these practices were mainly directed to the target plant (i.e. grapevine) and its surrounding area, we expected that these practices have influenced the soil alpha and beta bacterial and fungal diversity differently. Soil samples were collected from three different sites: row, inter-row (space between vines rows) and headland. The soil microbial community was investigated by targeted amplicon sequencing of the 16SrRNA gene (for bacteria) and the ITS region (for fungi), and the chemical and physical soil properties have been characterized. Soil samples collected in row and inter-row were chemically and microbiologically different from the headland soil (PERMANOVA: row/inter-row vs headland P ≤ 0.01), exhibiting this latter a significantly lower concentration of heavy metals. This soil heterogeneity seemed to play a crucial role in the variation of species diversity of microbial communities among sites (i.e. beta-diversity). In contrast, the mean species diversity in each site (i.e. alpha-diversity) did not change among the sites. The sole variation of the beta-diversity could indicate a possible turnover of soil microbial communities to agricultural practices without compromising the alpha-diversity values.