Deammonification’s performance and associated nitrous oxide emissions (N2O) depend on operational conditions. While studies have investigated factors for high performances and low emissions separately, this study investigated optimizing deammonification performance while simultaneously reducing N2O emissions. Using a design of experiment (DoE) method, two models were developed for the prediction of the nitrogen removal rate and N2O emissions during single-stage deammonification considering three operational factors (i.e., pH value, feeding and aeration strategy). The emission factor varied between 0.7 ± 0.5% and 4.1 ± 1.2% at different DoE-conditions. The nitrogen removal rate was predicted to be maximized at settings of pH 7.46, intermittent feeding and aeration. Conversely, emissions were predicted to be minimized at the design edges at pH 7.80, single feeding, and continuous aeration. Results suggested a weak positive correlation between the nitrogen removal rate and N2O emissions, thus, a single optimizing operational set-point for maximized performance and minimized emissions did not exist.