It is widely accepted that partial nitrification by ANAMMOX has the potential to become one of the key processes in wastewater treatment. However, large greenhouse gas emissions have been panobserved in many cases. A novel mesh separated reactor, developed to allow continuous operation of deammonification at smaller scale without external biomass selection, was compared to a conventional single-chamber deammonification sequencing batch reactor (SBR), where both were equally-sized pilot-scale reactors. The mesh reactor consisted of an aerated and an anoxic zone separated by a mesh. The resulting differences in the structure of the microbial community were detected by next-generation sequencing. When both systems were operated in a sequencing batch mode, both systems had comparable nitrous oxide emission factors in the range of 4% to 5% of the influent nitrogen load. A significant decrease was observed after switching from sequencing batch mode to continuous operation.