Aerobic sludge from the wastewater treatment plant was sampled as inoculation bacteria, and the effects of pH and initial Mn²⁺ concentration on the activation of manganese-oxidizing bacterium were studied. High-throughput sequencing technology was used to analyze the variation of microbial communities before and after activation. On this basis, the biogenic manganese oxides produced by manganese-oxidizing bacterium were characterized by X-ray diffraction. Besides, the effects of pH and biogenic manganese oxides dosage on the removal of EE2 by biogenic manganese oxides were analyzed. The results show that the best activation effect of manganese oxidizing bacterium is obtained when the initial Mn²⁺ concentration is 1 mmol/L at pH 7.0 and 83.3% Mn²⁺ is transformed into biogenic manganese oxides after 7 days under this condition. XRD results show that the biogenic manganese oxides produced mainly include MnO₂, Na₃Mn(PO₃)CO₃, and Mn₃O₄. According to the results of high-throughput sequencing, the abundance of Bacillus(0.75%), Acinetobacter(1.26%), Pseudomonas(1.36%), Sphingobacterium(1.81%), Flavobacterium(2.39%), Exiguobacterium(2.97%), Areomonas(7.35%) increases significantly, and the total relative abundance of typical manganese-oxidizing bacterium reaches 17.89%. When the biogenic manganese oxides dosage is 20 mg/L at pH 4.0, EE2 has the best removal efficiency. After 48 h, the removal rate of EE2 reaches 97.7%, in which 76.9% is removed by biogenic manganese oxides.