In this study, we compared two different types of decentralised systems in South East Queensland (SEQ) designed to produce Class A+ recycled water, and assessed their system robustness to shock loads, energy consumption and fugitive greenhouse gas (GHG) emissions. We found that through BioWin® modelling, the membrane reactor (MBR) system was relatively robust to hydraulic shock loads with tolerance up to 1.5 times of the design dry weather daily flow. However, the stability of nitrification process in MBR was significantly affected when the total nitrogen load in the influent increased by 30% while maintaining the constant inlet wastewater flow rate. For energy consumption, we found that the specific energy requirement for the MBR system was 6.1 kWh/kL of treated sewage, which was substantially higher than that for the other decentralised aerobic bio-filtration system (1.9 kWh/kL of treated sewage). We also used a mass balance approach to estimate the fugitive GHG emissions and concluded that electrical energy consumption data alone could substantially underestimate the overall GHG footprints for the decentralised systems. When the estimated CH4 fluxes were added to the energy consumption, the communal septic tanks with aerobic bio-filtration system generated a carbon dioxide equivalent footprint similar to that of the MBR system.