An innovative granular sludge deammonification system was incorporated into a conventional-activated sludge process. The process incorporated an internal baffle in the bioreactor for continuous separation of granular biomass from flocculent biomass, which allowed for controlling the solids retention time of flocculent sludge. The process was evaluated for ammonium removal from municipal digested sludge dewatering centrate under various operating conditions lasting over 450 days. The process successfully removed, on average, 90% of the ammonium from centrate at various ammonium loading reaching 1.4 kg/m3d at 20 hours hydraulic retention time. Controlling the retention time of the flocculent biomass and maintaining low nitrite concentration were both found to be effective for nitrite oxidizing bacteria management, resulting in a low nitrate concentration (below 50 mg/L) over a wide range of flocculent biomass concentration in the bioreactor.