Evaluating the sustainability of wastewater management alternatives is a challenging task. This paper proposes an innovative methodology to assess and compare the sustainability of four wastewater management alternatives: a) centralised water resource recovery facility (WRRF) based on activated sludge (AS); b) centralised WRRF with membrane bioreactors (MBR); c) decentralised WRRFs with upflow anaerobic sludge blanket reactors and trickling filters; d) centralised-decentralised hybrid system. In doing so, a composite indicator embracing total annual equivalent costs, carbon emission intensity, eutrophication and resilience (based on robustness and rapidity metrics) was developed using the analytic hierarchy process (AHP) method. The results show that decentralised and hybrid systems contribute less to carbon emission and eutrophication because of energy and fertilizer harvest and with a trade-off of higher costs of 7–17% than the ones of AS and MBR. In addition, decentralised and hybrid systems are more resilient, contributing to lower environmental impacts facing natural disasters. Based on the weights obtained by AHP, the decentralised alternative appears to be the most sustainable option due to its best performance in terms of carbon emission intensity and resilience. By contrast, the MBR alternative appeared the least sustainable evaluated wastewater management alternative. However, this alternative is sustainable option when the eutrophication criterion is heavily prioritized. The proposed approach contributes to the selection of the most sustainable wastewater management alternative from a holistic perspective.