This research elucidates the pollutants (nutrients and carbon) removal performance and nitrous oxide (N2O) emissions of two pilot plants. Specifically, a University of Cape Town (UCT) Membrane Bioreactor (MBR) plant and an Integrated Fixed Film Activated Sludge (IFAS)-UCT-MBR plant were investigated. The plants were fed with real wastewater augmented with acetate and glycerol in order to control the influent carbon nitrogen ratio (C/N). The short-term effect of the inlet C/N ratio variation (C/N = 5 mgCOD/mgN and C/N = 10 mgCOD/mgN) on the behaviour of both plants was investigated. The results showed that the IFAS-UCT-MBR configuration provided the best performance in terms of pollutants removal at the two investigated C/N ratios. Furthermore, the lowest N2O emission (with respect to the influent nitrogen) was observed in the IFAS-UCT-MBR configuration, thus suggesting a potential beneficial effect of the biofilm in the emission reduction. However, the membrane of the IFAS-UCT-MBR showed a greater fouling tendency compared to the UCT-MBR configuration. This result, likely related to the biofilm detached from carriers, could seriously affect the indirect GreenHouse Gas emissions due to the increase of the energy requirement for permeate extraction with the increase of membrane fouling.