Biogenic Mn oxides were prepared and purified using the Mn(II) oxidizing bacterium Providencia sp. LLDRA6, which was isolated from soil. Scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), X-ray diffraction (XRD), high-resolution transmission electron microscopy-selected area electron diffraction (HRTEM-SAED), X-ray photoelectron spectroscopy (XPS), and specific surface area (SSA) determination were used to characterize the biogenic manganese oxides. The biogenic manganese oxides were found to be poorly crystalline bixbiyte (Mn2O3) with a specific surface area of 5.740 m2/g. Biogenic Mn2O3 showed high adsorption capacity of Cu(II) and Zn(II), with an optimal pH of 6 and adsorption quantities of 89.889 mg/g and 70.595 mg/g, respectively. The adsorption curves of Cu(II) and Zn(II) by biogenic Mn2O3 were both consistent with the pseudo-second kinetic model, indicating that chemisorption influenced both Cu(II) and Zn(II) adsorption rates. Cu(II) and Zn(II) adsorption by biogenic Mn2O3 followed the Langmuir isothermal adsorption model, suggesting that the adsorption processes belonged to monomolecular layer adsorption.