Suspended sludge deammonification technologies are frequently applied for sidestream ammonia removal from dewatering liquors resulting from a thermal hydrolysis anaerobic digestion (THP/AD) process. This study aimed at optimizing the operation, evaluate the performance and stability of a full-scale suspended sludge continuous stirred tank reactor (S-CSTR) with a hydrocyclone for anaerobic ammonia oxidizing bacteria (AMX) biomass separation. The S-CSTR operated at a range of nitrogen loading rates of 0.08−0.39 kg N m−3 d−1 displaying nitrogen removal efficiencies of 75−89%. The hydrocyclone was responsible for retaining 56−83% of the AMX biomass and the washout of ammonia oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was two times greater than AMX. The solid retention time (SRT) impacted on NOB washout, that ranged from 0.02−0.07 d−1. Additionally, it was demonstrated that an SRT of 11−13 d was adequate to wash-out NOB. Microbiome analysis revealed a higher AMX abundance (Candidatus scalindua) in the reactor through the action of the hydrocyclone. Overall, this study established the optimal operational envelope for deammonification from THP/AD dewatering liquors and the role of the hydrocyclone towards maintaining AMX in the S-CSTR and hence obtain process stability.