Abstract: The thermal hydrolysis process (THP) has been proven to be an excellent pretreatment step for an anaerobic digester (AD), increasing biogas yield and decreasing sludge disposal. The goal of this work was to optimize deammonification for efficient nitrogen removal despite the inhibition effects caused by the organics present in the THP-AD sludge filtrate (digestate). Two sequencing batch reactors were studied treating conventional digestate and THP-AD digestate, respectively. Improved process control based on higher dissolved oxygen set-point (1 mg O-2/L) and longer aeration times could achieve successful treatment of THP-AD digestate. This increased set-point could overcome the inhibition effect on aerobic ammonium-oxidizing bacteria (AerAOB), potentially caused by particulate and colloidal organics. Moreover, based on the mass balance, anoxic ammonium-oxidizing bacteria (AnAOB) contribution to the total nitrogen removal decreased from 97 +/- A 1 % for conventional to 72 +/- A 5 % for THP-AD digestate treatment, but remained stable by selective AnAOB retention using a vibrating screen. Overall, similar total nitrogen removal rates of 520 +/- A 28 mg N/L/day at a loading rate of 600 mg N/L/day were achieved in the THP-AD reactor compared to the conventional digestate treatment operating at low dissolved oxygen (DO) (0.38 +/- A 0.10 mg O-2/L).