Previous works on Membrane Aerobic Biological Reactors (MABR) CoMANDR 1.0, CoMANDR 2.0, and R-CoMANDAR have demonstrated their ability to stabilize various space based waste streams over operating periods of ~1 year. Biological pretreatment by MABR systems can stabilize space based waste streams. Biological stabilization includes reducing the pH, conversion of organic N to NOx- and oxidation of dissolved organic matter to CO2. These processes produce a more stable waste product (brine), facilitate the distillation processes, and enable evaporative or membrane based systems. An alternative to aerobic operation would be to include anoxic operation to promote denitrification and production of N2 gas. This results in a reduced O2 demand and increases ammonia oxidation efficiency. Denitrifictaion can be accomplished in either a single reactor (Simultaneous Nitrification Denitrification) or in a two-stage system with separate aerobic and anoxic reactors. We evaluated the performance of both architectures in pilot scale systems (1-2 crew/d). Each system was continuously operated for over 2 years during which they processed a variety of habitation waste streams (ISS, Transit, and EPB) in both a continuous and on production feed mode. Here we report the results of the two stage system. Results indicate that the two stage system can successfully remove organic carbon, lower pH and convert organic N to N2 gas. Organic carbon and organic N oxidation reaction rates for the two stage system are similar to past studies for single stage aerobic systems. The two stage system is more complex and requires an additional pump. While no maintenance was required on the system during the nearly two year period of operation, the packed bed did produce N2 gas for many operational test points. The performance and comparison of operational conditions are detailed below