Aerobic granular sludge sequencing batch reactor (SBR) technology constitutes an attractive solution for the simultaneous removal of biodegradable carbonaceous (C), phosphorous (P) and nitrogenous (N) loads from food-industrial and municipal wastewaters. Besides reactor design and operational parameters, the overall treatment performance is linked to the biofilm properties, and to the dynamics and metabolic activities of microbial communities interacting within the biofilm. The influence of two different activated inoculation sludges was tested for the start-up of aerobic granular sludge SBRs, in relation to process parameters. Four acetate-fed bubble column SBRs were run under mesophilic conditions. The produced biofilm structures were analyzed by microscopy. The bacterial community dynamics were characterized by terminal restriction fragment length polymorphism (T-RFLP). Cloning and sequencing of terminal restriction fragments (T-RFs) resulted in the identification of bacterial species involved in the process. The first inoculum, taken from a C-P-N biologically treating WWTP rich in slow growing phosphate (PAO) and glycogen accumulating organisms (GAO), favoured the production of PAO-enriched dense fast settling granules, under low aeration velocity (0.018 m/s). Stable C and P removal was obtained. With the second inoculum, low in PAO/GAO, fast growing filamentous heterotrophic microorganisms were dominant (T-RF 210-211 bp). Slow settling bulking granules were produced, and washed out rapidly. External filamentous growth could be prevented by applying a higher shear stress (0.040 m/s), but the segmented chain Gram-negative filamentous bacterium Flexibacter sp. type 0411 (T-RF 198-199 bp) dominated the granule core. Phosphorus was not removed. From a process development point of view, the choice of a high quality inoculum is crucial for the production of dense aerobic granules at low aeration velocity, resulting in advantages such as aeration energy savings, and simultaneous COD and phosphorus removal. Enhanced treatment performances can then be obtained by optimizing further process parameters in addition to the inoculum quality.