SBR technology is used to treat the supernatant from mesophilic anaerobic digestion of piggery wastewater. The novelty of the treatment consists in the use of a final coagulation/flocculation step inside the SBR cycle to reach the legal COD effluent standard. The pH changes introduced by the use of FeCl3 do not affect the nitrifying activity. The SBR treatment includes a strategy to the control of oxygen supply and ammonia concentrations inside the digester to favor the biological nitrogen removal over nitrite, which makes the process more economical. The influence of several of these parameters on the AOB biomass activity is studied in this paper.