The main challenge in implementing shortcut nitrogen removal processes for mainstream wastewater treatment is the out-selection of nitrite oxidizing bacteria (NOB) to limit nitrate production. A model-based approach was utilized to simulate the impact of individual features of process control strategies to achieve NO−2-N shunt via NOB out-selection. Simulations were conducted using a two-step nitrogen removal model from the literature. Nitrogen shortcut removal processes from two case studies were modeled to illustrate the contribution of NOB out-selection mechanisms. The paper highlights a comparison between two control schemes; one was based on online measured ammonia and the other was based on a target ratio of 1 for ammonia vs. NOx (nitrate + nitrite) (AVN). Results indicated that the AVN controller possesses unique features to nitrify only that amount of nitrogen that can be denitrified, which promotes better management of incoming organics and bicarbonate for a more efficient NOB out-selection. Finally, the model was used in a scenario analysis, simulating hypothetical optimized performance of the pilot process. An estimated potential saving of 60% in carbon addition for nitrogen removal by implementing full-scale mainstream deammonification was predicted.