The short-cut nitrogen removal (SCNR) and denitrifying phosphorus removal via nitrite (DPRN) were studied using a pilot-scale sequencing batch reactor (SBR) for the treatment of the supernatant produced from the anaerobic co-digestion of waste activated sludge (WAS) and the organic fraction of municipal solid waste (OFMSW). The stability and behaviour of the biological via-nitrite processes were examined under transient conditions, imposed from the ordinary and extraordinary operation of the full-scale anaerobic digestion plant and the dewatering process of the anaerobic digestate. Nutrients removal was tested at low volumetric nitrogen loading rates (vNLR = 0.2 kgN m-3 d-1), at the vNLR of the system's nitrifying capacity (0.8 kgN m-3 d-1) and above its nitrifying capacity (1.1 kgN m-3 d-1). Complete absence of nitrite oxidizing bacteria (NOB) activity was accomplished, even when the free ammonia (FA) concentration in the reactor was very low (<0.45 mgNH3-N L-1). The type of external carbon source critically impacted on the specific nitrite uptake rate (sNUR) and DPRN with fermentation liquid from OFMSW and from cattle manure and maize silage (CM&MS) to enhance these processes.