Background The role of soil microbiomes in agriculture is now becoming more and more important, leading to definition of plants as complex organisms formed by the plant itself plus the microbes inhabiting its tissues, the surface of every organ and the ones living adhered or in proximity of the roots. In this context it is important to define the factors able to influence the composition of such microbial communities. In addition, as already demonstrated, the microbial community associated to a specific soil is able to predetermine the health status of the crops in the future. For this reason, we decided to investigate how the soil geological characteristics can influence the microbial community associated to the close geographical related vineyard.Results We decided to analyse a calcarenitic and a marly-limestone soil which are both typical of the viticulture in the Menfi area (Sicily, Italy). Moreover, since vineyard is a semi-anthropic environment we decided to investigate both the top (10-20 cm) and deep (120 cm) soil layers as anthropic influenced and almost-undisturbed soil respectively. Interestingly we observed that, despite the close geographical proximity, the soil microbiomes were slightly different and that in addition, the soil geological characteristics are able to influence the root distribution and the accumulation of both pathogen- and symbiont-related genera. Furthermore, sensory profiles of the Grillo wines obtained from the two different soils confirmed the tight link between soil origin and wine traits.Conclusions In contrast to what observed in other works we pointed out that the geological characteristics of soils can have an important influence on soil microbial composition and assemblage in close geographical related vineyards, with a potential effect on wine features. Furthermore, defining the microbial composition of agricultural soils it’s a crucial step to achieve a more sustainable agriculture and viticulture. In this optic, the observed link between the geological characteristics and the microbiome profiles need to be taken into account when considering a soil for the successful establishment low chemical input agriculture practices.The SRA accession numbers of the NGS reported in this paper are deposited in NCBI under the BioProject PRJNA655455; BioSample SAMN15735114 and SAMN15735115; SRA accession SRR12436974 and SRR12436973