The formation of manganese oxides in nature is commonly mediated by microorganisms. In this study, the mineralization of biogenic manganese oxidation mediated by Pseudomanas putida has been experimentally investigated by employing various characterization techniques, including SEM, FESEM, TEM, XRD, and STXM-NEXAFS. The results indicate that Mn2+ ions can be oxidized into Mn(IV) minerals (birnessite and pyrolusite) and Mn(III) minerals (hausmannite and feitknechtite), successively. The primary products (birnessite and pyrolusite) further transformed into hausmannite and feitknechtite under Mn2+ ion-enriched conditions. However, birnessite and pyrolusite are the end-products of the continuous microbial oxidation processes. These biogenic Mn oxides are poorly crystallized, which provides them with a high potential for usage in environmental restoration of contaminated soils and waters contaminated with heavy metals. The approaches employed in this study will also enrich genesis research of biological oxidation of Mn(II) species in nature.