The pollution of multifarious pollutants such as heavy metal, organic compounds, and nitrate are a hot research topic at present. In this study, the functions of Zoogloea sp. MFQ7 and its biological precipitation formed during bacterial manganese oxidation on the removal of phenol and 17β-estradiol (E2) were investigated. Strain MFQ7, a manganese-oxidizing bacteria, can remove 98.34% of phenol under pH of 7.1, a temperature of 30 ℃ and Mn2+ concentration of 24.34 mg L−1, additionally, the optimum E2 removal by strain MFQ7 was 100.00% at pH of 7.1, temperature of 28 ℃ and Mn2+ concentration of 28.45 mg L−1 by using response surface methodology (RSM) based on Box-Behnken design (BBD) model. The maximum adsorption capacity of bio-precipitation for phenol and E2 was 201.15 mg g−1 and 65.90 mg g−1, respectively. Furthermore, adsorption kinetics and isotherms analysis, XPS, FTIR spectra, Mn(III) trapping experiments elucidated chemical adsorption and Mn(III) oxidation contribute to the removal of phenol and E2 by biogenic manganese oxides. These findings indicated that the adsorption and oxidation of manganese are expected to be one of the effective means to remove these typical organic pollutants containing phenol and E2.