Sulfidized nanoscale zero-valent iron (S-nZVI) is a promising material for in situ soil remediation. However, its transformation (i.e., aging) and effects on the microbial community in soil ecosystems are largely unknown. In this study, S-nZVI having low (S-nZVI (L)) and high sulfur-doping (S-nZVI (H)) were incubated in soil microcosms and bare nZVI was used as a control. Their aged products were characterized using microspectroscopic analyses and the changes in the corresponding soil microbial community were determined using high-throughput sequencing analyses. The results indicate that severe corrosion of both bare and S-nZVI occurred over 56 days of aging with significant morphological and mineral changes. Magnetite, lepidocrocite, and goethite were detected as the main aged products. In addition, sulfate ions, pyrite, and iron polysulfide were formed in the aged products of S-nZVI. Cr(VI) removal test results indicated that S-nZVI(L) achieved the best results after aging, likely because of the optimal FeS arrangement on its nanoparticle surfaces. The presence of nZVI and S-nZVI increased the abundance of some magnetotactic microorganisms and altered bacterial and fungal community structures and compositions. Moreover, the addition of S-nZVI enriched some bacterial and fungal genera related to sulfur cycling because of the presence of sulfide-bearing material. The findings reveal the transformation of S-nZVI during aging and its effects on microbial communities in soil ecosystems, thereby helping to the evaluation of S-nZVI application in soil remediation.