The evolution of removal performance and bacterial population dynamics of an aerobic granular sequencing batch reactor were investigated during stable operation and reactivation after prolonged storage. The system was run for a period of 130 days including the stable condition phase, storage period and the subsequent reactivation process. Excellent removal performance was obtained during the stable operation period, which was decayed by the extended idle conditions. The removal efficiencies for both carbon and nitrogen decayed while phosphorus removal remained unaffected. Both granules structure and physical properties could be fully restored. Microbial populations shifted sharply and the storage perturbations irreversibly altered the microbial communities at different levels. Extracellular polymeric substances (especially protein) and key groups were identified as contributors for storage and re-startup of the aerobic granular system. (C) 2017 Elsevier Ltd. All rights reserved.