The manganese Mn(II) oxidizing by Shewanella oneidensis MR-1 (MR-1) underlines a new pathway for Mn nanoparticle synthesis. However, the mechanism of Mn oxidizing and the compositions of biogenic products remain unknown. Here, the oxidation of Mn(II) to Mn2O3 nanoparticles was discovered, and was to be driven by cytochrome c reductase Complex III. According to the transcriptomic analysis, genes encoding Complex III were upregulated during the Mn(II) oxidizing process, corresponding to the inability of mutants ΔpetC and ΔpetA (Complex III subunits). The morphology and activity of Mn2O3 particles were further controlled by the extracellular electron transfer of MR-1, associated with the change of the shape from nanoparticle to nanosheet and with stronger electron transfer ability, and eventually led to a 1.5-fold higher methylparaben degradation rate by activating peroxymonosulfate radical oxidizing effectively. Our work provides insights into the Mn-oxidizing mechanism and modification of biogenic Mn for pollutant removal.