The aerobic granular sludge process optimization is linked to the interdependence of process, biofilm and microbial scales. Stable dense fast-settling granules composed of bacterial guilds for the simultaneous removal of carbonaceous, phosphorous and nitrogenous loads are desired. In this study, two activated inoculation sludges were used to start-up aerobic granular sludge bubble column sequencing batch reactors, one from a wastewater treatment plant (WWTP) that removes carbon biologically, nitrifies, and removes phosphorous chemically, and one from a WWTP removing all nutrients (C-P-N) biologically. The use of the former inoculum in reactors with low upflow aeration velocity (0.018 m s-1) resulted in the wash-out of slow-settling filamentous bulking granules, dominated by heterotrophic filamentous bacterial strains (Leptothrix or Sphaerotilus sp.), independently from pulse or anaerobic acetate-feeding modes. Granules with relatively good settling properties could only be obtained at high aeration velocity (0.040 m s-1), however the granule cores were still dominated by filamentous Flexibacter sp. Well settling aerobic granules were obtained at low aeration velocity with the inoculation sludge from the latter WWTP in combination with alternate anaerobic feeding and aerobic starvation, indicating that the inoculum was of crucial importance for a stable aerobic granular sludge process operated with low impact process parameters.