Submerged membrane bioreactors (MBRs) have attracted a significant amount of interest for decentralised treatment systems due to their small footprint and ability to produce high quality effluent, which is favourable for water reuse applications. This study provides a comprehensive overview of the capacity of a full-scale decentralised MBR to eliminate 17 endocrine disrupting chemicals (EDCs) and five indigenous microbial indicators. The results show that the MBR consistently achieved high removal of EDCs (>86.5%). Only 2 of the 17 EDCs were detected in the MBR permeate, namely two-phenylphenol and 4-tert-octylphenol. Measured log10 reduction values of vegetative bacterial indicators were in the range of 5–5.3 log10 units, and for clostridia, they were marginally lower at 4.6 log10 units. Removal of bacteriophage was in excess of 4.9 log10 units. This research shows that MBRs are a promising technology for decentralised water reuse applications.