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Soil microbes have critical influence on the productivity and sustainability of agricultural ecosystems, yet the magnitude and direction to which management practices affect the soil microbial community remain unclear. This work aimed to examine the impacts of three farming systems, conventional grain cropping (CON), organic grain cropping (ORG), and grain cropping-pasture rotation (ICL), on the soil microbial community structure and putative gene abundances of N transformations using high-throughput 16S rRNA gene and ITS sequencing approaches. Two additional systems, a forest plantation (PF) and an abandoned agricultural field subject to natural succession (SUC), were also included for better assessment of the soil microbial community in terms of variation scale and regulatory importance of management intensity vs. plant type. Farming systems significantly affected the biodiversity of soil fungi but not bacteria, with Shannon index being the lowest in ORG. Bacterial and fungal communities in three cropping systems clustered and separated from those in PF and SUC, suggesting that management practices as such played minor roles in shaping the soil microbial community compared to plant type (i.e., woody vs. herbaceous plants). However, management practices prominently regulated habitat-specific taxa. <i>Lecanoromycetes</i>, a class of <i>Ascomycota</i> accounted for ∼10% of total fungal population in ORG, but almost nil in the other four systems. ORG also enriched bacteria belonging to the phyla, <i>Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi</i>, and <i>Gemmatimonadetes</i>. Further, PICRUSt predicted that N-cycle community compositions varied with farming systems; compared to CON, ORG and ICL were more divergent from PF and SUC. Soil pH, together with inorganic N, extractable organic C, and soil organic C:N ratio explained < 50% of the total variations in both bacterial and fungal communities. Our data indicates that while moderately affecting the overall structure of the soil microbial community, management practices, particularly fertilization and the source of N (synthetic vs. organic), were important in regulating the presence and abundance of habitat-specific taxa.