The successful development of aerobic granular sludge (AGS) for secondary wastewater treatment has been linked to a dedicated anaerobic feeding phase, which enables key microbes such as poly-phosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms to gain a competitive advantage over floc-forming organisms. The application of AGS to treat high-saline sewage and its subsequent impacts on microbial ecology, however, are less well understood. In this study, the impacts of high-saline sewage on AGS development, performance and ecology were investigated using molecular microbiology methods. Two feeding strategies were compared at pilot scale: a full (100%) anaerobic feed; and a partial (33%) anaerobic feed. The results were compared to a neighbouring full-scale conventional activated sludge (CAS) system (100% aerobic). We observed that AGS developed under decreased anaerobic contact showed a comparable formation, stability and nitrogen removal performance to the 100% anaerobically fed system. Analysis of the microbial ecology showed that the altered anaerobic contact had minimal effect on the abundances of the functional nitrifying and denitrifying bacteria and Archaea; however, there were notable ecological differences when comparing different sized granules. In contrast to previous work, a large enrichment in PAOs in AGS was not observed in high-saline wastewater, which coincided with poor observed phosphate removal performance. Instead, AGS exhibited a substantial enrichment in sulfide-oxidising bacteria, which was complemented by elemental analysis that identified the presence of elemental sulfur precipitation. The potential role for these organisms in AGS treating high-saline wastewater is discussed.