Partial nitritation anammox (PNA) membrane aerated biofilm reactors (MABRs) have the potential to be employed in mainstream wastewater treatment and can drastically decrease the energy and carbon requirements for nitrogen removal. Previous PNA MABR studies have looked at 1-stage systems, but no study has holistically compared the performance of different MABR configurations. In this study, a PNA MABR was mechanistically modelled to determine the impact of the reactor configuration (1-stage, hybrid, or 2-stage system) on the location of the preferred niche for anammox bacteria and the overall nitrogen removal performance. Results from this study show that the 2-stage configuration, which used an MABR with a thin biofilm for nitritation and a moving bed biofilm reactor for anammox, had a 20% larger nitrogen removal rate than the 1-stage or hybrid configurations. This suggests that an MABR should focus on maximizing nitrite production with anammox implemented in a second-stage biofilm reactor to achieve the most cost-effective nitrogen removal. However, the optimal configuration will likely be facility specific, as each facility differs in operating costs, construction costs, footprint, and effluent limits. Additional experimentation is required to confirm these results, but this work narrows the number of viable configurations that need to be tested. The results of this study will inform researchers and engineers how to best implement PNA MABRs in mainstream nitrogen removal at larger scales.