Centralized systems employ biological treatments to remove nutrients, whereas decentralized systems, especially in rural areas, face challenges in implementing them. These systems are low flow but high carbon and nitrogen concentrations, and low C/N ratios. Source-separated wastewater (urine + flush) is an extreme example, like confined animal-feeding wastewater. High nutrient concentrations necessitate innovative technologies typically not employed for decentralized systems. This research demonstrates a simple two-stage nitritation-anammox system to treat high N concentration wastewater (pure urine + flush water). The systems consisted of a Membrane Aerated Biological Reactor (MABR) which performed carbon oxidation and nitritation and novel anammox reactors, (Pancopia AnammoX (PAXs)). The MABRs achieved OC removal over 108–198 g-C/m3-day with ∼ 97% removal, TAN oxidation rates up to 156 g-N/m3-day and nitrite/AN ratios were near 1 with no external control (e.g. pH, DO, cell wasting) other than urine loading rate. The PAXs achieved maximum AN removal efficiencies of 85–97%. The main limitation to complete TN removal in the PAXs was insufficient NO2- in the influent (nonideal influent NO2-/AN ratio). This system was not optimized for energy efficiency and had low volumetric conversion rates compared with other systems. However, it demonstrates that source-separated wastewater can be effectively treated with near complete N removal using a system with minimal process control requirements, lack of solid production, and elimination of diffuse aeration preventing odor generation. These attributes are attractive for applications where conditions do not allow for more complex high-rate systems such as developing societies and rural areas.