Abstract: Deammonification systems are being implemented as cost- and resource-efficient nitrogen removal processes. However, their complexity is a major hurdle towards successful transposition from side- to mainstream application. Merely out-selecting nitrite oxidizing bacteria (NOB) or retaining anammox bacteria (AnAOB) does not guarantee efficient mainstream deammonification. This paper presents for the first time the interactions and synergies between kinetic selection, through management of residual substrates, and physical selection, through separation of solid retention times (SRTs). This allowed the formulation of tangible operational recommendations for successful deammonification. Activity measurements were used to establish retention efficiencies (η) for AnAOB for full-scale cyclones and rotating drum screens installed at a sidestream and mainstream deammonification reactor (Strass, Austria). In the sidestream reactor, using a screen (η = 91%) instead of a cyclone (η = 88%) may increase the capacity by up to 29%. For the mainstream reactor, higher AnAOB retention efficiencies achieved by the screen (η = 72%) compared to the cyclone (η = 42%) induced a prospective increase in capacity by 80–90%. In addition, the switch in combination with bioaugmentation from the sidestream made the process less dependent on nitrite availability, thus aiding in the outselection of NOB. This allowed for a more flexible (intermittent) aeration strategy and a reduced need for tight SRT control for NOB washout. A sensitivity analysis explored expected trends to provide possible operational windows for further calibration. In essence, characterization of the physical selectors at full scale allowed a deeper understanding of operational windows of the process and quantification of capacity, ultimately leading to a more space and energy conservation process.