The Soil Health Experiment (SHE) used in this study represents an unique system to compare the long-term effects of conventional and organic systems and on microbial community diversity and assembly. The present study was conducted to identify the major forces of the long-term impact (> 8 years) of conventional and organic farming systems and the effect of SHTs (untreated for > 8 years) on microbial community diversity and assembly. Hence, we hypothesize that organic systems can hold higher microbial diversity than conventional system and there is legacy effect on microbial community assembly and soil niche differentiation promoted by soil long-term soil management. To test this hypothesis we assigned the fungal and protists community. Our results showed that organic farming systems had the highest impact in promoting the diversification of microbial taxonomic and phylogenetic diversities. However, we detect a legacy effect of the different soil management treatments in generated a variety of niches that were filled by an group of habitat specialists. Our ability in apply a multidisciplinary approach to monitor microbial community traits provide insight to manage agro-ecosystems by promoting beneficial microbial community assemblages for soil health and productivity.