An induced sludge bed anaerobic reactor system that includes at least two stages of bioreactor processing, a first-stage feeding system, a second-stage feeding system, a pH balancing system, an effluent recirculation system, a gas management system, at least one nitrogen reduction system, and a controller. In addition, the nitrogen reduction system(s) if configured for reducing an amount of one or more nitrogen compounds in a substrate mixture sufficient to procedure a non-toxic substrate mixture with respect to anaerobic digestion of the non-toxic substrate by the induced sludge bed anaerobic reactor system.