Over the last decade significant studies have determined the community structure of soil microbial communities from the poles to the tropics. However, linking this structure to underlying niche and neutral drivers remains a significant challenge. In this study we addressed this by taking three cutting-edge approaches: (i) sampling according to a hierarchically nested design, (ii) analysis of taxa at fine taxonomic resolution using amplicon sequence variants, and (iii) application of the new multi-site diversity metric zeta diversity. We demonstrate that, at fine taxonomic resolution, soil microbial communities undergo a high rate of compositional turnover. They appear to be structured primarily by niche-based assembly processes driven by soil physicochemical factors. We also observed that broadening taxonomic resolution and filtering rare taxa causes a fundamental shift in the occupancy-frequency distribution, significantly slowing the rate of compositional turnover and causing false signals of stochastic community assembly. Our findings suggest that the interpretation of underlying niche and neutral process driving microbial turnover is highly dependent on taxonomic resolution and filtering rare taxa. Moreover, these findings suggest that microbial communities exhibit much stronger biogeographical patterns than previously recognised.