AbstractBACKGROUNDIn this study, an onsite pilot sequencing batch reactor (SBR) of 450 L was operated at a local Flemish slaughterhouse in two consecutive periods. During period I, nitrogen removal via nitritation/denitritation (Nit/DNit) was achieved by the use of an innovative startup strategy without seed sludge and subsequently maintained by the use of aeration phase length control based on the oxygen uptake rate (OUR). In period II, the operational strategy was modified. In order to obtain Nit/DNit granular sludge (GS), an anaerobic (feast) feeding was introduced followed by a dynamic controlled (OUR‐based) aerobic (famine) reaction step.RESULTSAfter 74 days, the local (Flemish) legislation standards for COD (125 mg O2 L−1) and T‐N (15 mg N L−1) were fulfilled. During period II, floccular sludge was partially transformed into GS, which resulted in increased COD and NH4‐N conversion rates of 50 and 60% respectively. Average removal efficiencies for SCOD, N and P during period II were 89.5 ± 4.2, 88.8 ± 9.8 and 84.4 ± 9.3% respectively. Despite the relatively low biomass concentrations (2.5 g L−1), excellent sludge settling was reported, with SVI30 < 100 mL g−1 from day 167 onwards. Moreover, it was found that the operational strategy and temperature variability had a crucial impact on the microbial community dynamics and granule growth.CONCLUSIONThis study demonstrated the Nit/DNit BNR‐GS system in a real operational environment through the operation of an onsite pilot plant. © 2019 Society of Chemical Industry