A 500-day comparative study with a novel membrane bioreactor (NMBR), anaerobic-anoxic-aerobic (A2/O) process, and University of Cape Town-adapted MBR (UMBR) investigated the effect of membrane on effluent dissolved organic nitrogen (efDON) using synthetic (SWW) and municipal wastewater (MWW). The runs, comparing an NMBR and A2/O process, indicated 0.3 mg/L lower efDON in the former than the latter. However, NMBR and UMBR achieved similar efDON quality, with an average of 0.8 mg/L, and the DON reduction by membrane averaged 0.4 mg/L, while the A2/O efDON was slightly higher than DON in the aeration tank, by 0.08 mg/L, on average. The efDON during the MWW run increased by as much as 0.8 mg/L compared with the SWW run. The efDON is a component of a protein found in soluble microbial products, and it followed a cyclical temporal pattern during the runs. Membrane fouling propensity increased the efDON. This study presents evidence that membranes are effective in reducing efDON.