We developed a lab-scale aerobic–methane oxidation bioreactor (MOB)–anoxic system, combining a MOB and the aerobic–anoxic denitrification process, and evaluated its potential for advanced nitrogen treatment in wastewater treatment plants (WWTPs). The MOB used biogas generated from a WWTP and secondary-treated wastewater to support mixed methanotroph cultures, which mediated the simultaneous direct denitrification by methanotrophs and methanol production necessary for denitrifying bacteria in the anoxic chamber for denitrification. Compared to the aerobic–anoxic process, the aerobic–MOB–anoxic system with an influent concentration of 4.8 L·day−1 showed a marked increase in the reduction efficiency for total nitrogen (41.9% vs. 85.9%) and PO4−3-P (41.1% vs. 69.5%). However, the integrated actions of high nitrogen and phosphorus consumption are required for methanotroph growth, as well as the production and supply of methanol as a carbon source for denitrification and methane monooxygenase-mediated oxidation of NH3 into N2O by methanotrophs. After three months of continuous operation using actual wastewater, the total nitrogen removal rate was 76.3%, equivalent to the rate observed in a tertiary-advanced WWTP, while the total phosphorus removal rate reached 83.7%.