Methods and systems are provided for treating wastewater to simultaneously remove nitrogen, carbon, and phosphorus, while recovering energy in the form of methane and carbon dioxide. An ammonia-containing stream is directed to a pretreatment tank that produces excess sludge, biogas, and a pretreated stream. The pretreated stream has at least 45% less carbon than the ammonia-containing stream. The pretreated stream is then directed to an anoxic tank, which promotes phosphorus release and fermentation of particulate and dissolved organic matter. The mixed liquor is transferred to an aerated tank having low dissolved oxygen concentrations to promote development of phosphorus-release bacteria that is eventually recycled to the anoxic tank by way of the return activated sludge. Simultaneous nitrification, denitrification, and phosphorus release occur in the aerated tank. A membrane tank separates treated effluent from activated sludge in a membrane tank.