While the peroxymonosulfate (PMS) advanced oxidation was regarded as an emerging method to degraded recalcitrant pollutant in soil, the design and synthesis of activator for PMS was still challenging. Here, by using Shewanella oneidensis MR-1, a representative model strain of dissimilatory metal reducing bacteria in soil and sediment, biogenic Mn2O3 nanoparticles was synthesized by the oxidizing of 5 mM Mn(II), to activate the PMS for phenanthrene degrading in soil. It was observed that 77.4% of phenanthrene was removed in soil with biogenic Mn2O3 whereas 55.7% was achieved with chemical synthesized Mn2O3, which was associated with their characterizations: biogenic Mn2O3 presenting faster electron transfer rate and owing to the higher ratio of Mn(III) to donate electrons to PMS. Moreover, the feasibility of this PMS advanced oxidation to soil remediation was further evaluated by the analysis of microbial community diversity. Considering that Mn is abundant in natural soil and groundwater system, biogenic Mn2O3 synthesized in-situ would be a new strategy for soil remediation.