Abstract: The effect of free ammonia (NH3 or FA), free nitrous acid (HNO2 or FNA), and total alkalinity (TA) on the performance of a partial nitrification (PN) sequencing batch reactor (SBR) treating anaerobically pretreated pig slurry was studied. The SBR was operated under alternating oxic/anoxic (O/A) conditions and was fed during anoxic phases. This strategy allowed using organic matter to partially remove nitrite (NO2-) andnitrate (NO3-) generated during oxic phases. The desired NH4+ to NO2- ratioof 1.3gN/gNwas obtained when an Ammonium Loading Rate (ALR) of 0.09 gNH(4)(+)N/L d was applied. The system was operated at a solid retention time (SRT) of 15-20 d and dissolved oxygen (DO) levels higher than 3 mg O-2/L during the whole operational period. PN mainly occurred caused by the inhibitory effect of FNA on nitrite oxidizing bacteria (NOB). Once HNO2 concentration was negligible, NH4+ was fully oxidized to NO(3)(-)in spite of the presence of FA. The use of biomass acclimated to ammonium as inoculum avoided a possible effect of FA on NOB activity.