This paper presents a comprehensive study on a Membrane BioReactor - Integrated Fixed Film Activated Sludge - Intermittent Aeration (MBR-IFAS-IA) pilot plant. The MBR-IFAS-IA operated under three different sludge retention times (SRTs): 7.0, 3.5 and 2.5 days during Period I, II and III, respectively. The pilot plant operated in intermittent aeration operation mode to achieve an advanced wastewater treatment for net zero carbon emissions. A comprehensive monitoring campaign was carried out measuring several parameters: carbon, nitrogen, phosphorus, extracellular polymeric substances, kinetics by respirometry tests, greenhouse gas emissions and fouling. The total chemical oxygen demand removal was very high (97.8% on average). An improvement in orthophosphate removal efficiency occurred during Period II (43.8%) compared to Period I (27.7%). However, a worsening in the removal efficiency performances was obtained in periods with lower SRT (Period III), mainly for ammonia oxidation and total nitrogen (TN). Moreover, the reduction of SRT from 7.0 to 2.5 days showed a substantial worsening in the membrane fouling (mostly in irreversible fouling).