Soil microbial communities are site-specific and vary in response to changing environmental conditions. Thus, there are dissimilar microbial communities under different environmental conditions. Additionally, tree roots recruit specific microbial partners from the local soil communities. From then on, the host tree represents a major nutrient source for its root-associated microbes. Hence, tree root-associated microbiome is shaped by both the host tree and local environmental conditions. However, there are only few studies on microbial distribution at larger scale, and knowledge on the respective impacts of host plant and site specificities is still scarce. On this background, we analyzed the soil microbiomes in the root vs. root-free zones of genetically identical host tree saplings, called PhytOakmeter (Quercus robur L., clone DF159), outplanted at four grassland field sites across a European North-South transect, ranging from Finland to France. Soil microbial DNA was extracted from soil samples of the four sites, bacterial 16S and fungal ITS2 were amplified, and sequenced using Illumina MiSeq. Microbial communities were analysed in relation to geographic, soil physico-chemical and host tree parameters. Regardless of PhytOakmeter presence or absence, bacterial diversity was impacted by abiotic environmental parameters, and increased southwards. Fungal diversity was constant in the PhytOakmeter root zone, and the abiotic environmental parameters showed only an impact in the tree root-free zone. The bacterial and fungal communities were site-specific, impacted by numerous biotic and abiotic parameters as well as by the interplay among them, and positively correlated to each other in both the soil compartments. Another striking finding is the relationship found between PhytOakmeter growth and the tree root zone microbiome. However, PhytOakmeters less impacted the microbial communities compared to geographic and soil physico-chemical parameters. Our findings revealed complex interactions between PhytOakmeter and several abiotic environmental parameters in shaping the tree root zone microbial community.