Aerobic granular sludge (AGS) biofilm process is a sustainable technology for full biological nutrients removal (BNR) from municipal and agro-industrial wastewater, and for secondary clarification in single sequencing batch reactors (SBR). Fundamental research on the structure and dynamics of microbial communities inside AGS biofilms remains to be performed in addition to full-scale implementation, in order to link process conditions and reactor efficiency, and to tailor metabolic activities for stable treatment performance. Ten bubble column SBRs were run during three successive campaigns for (i) cultivating AGS, (ii) optimizing the AGS biofilm stability, and (iii) investigating process conditions favouring full BNR. Molecular ecology analyses on eubacterial communities performed during each first month of start-up revealed that optimally dense and fast-settling AGS biofilms were composed of 60-90% of Zoogloea sp. of the β-proteobacterial order Rhodocyclales, and of less than 20% of undesired Burkholderiales filamentous bulking heterotrophic bacteria. Zoogloea sp. was favourably selected by combining optimal process parameters: inoculum from a full BNR plant, 20°C, 60min- slow plug-flow anaerobic influent feeding regime, 0.018 m s-1 air superficial velocity, and settling time lower than 5 min. The application of a short settling phase induced a washout dynamics between the times of SBR inoculation and AGS nucleation. This low initial sludge retention time selected for a fast-settling biomass, but hampered the growth of relevant phosphorus-accumulating organisms, nitrifiers and denitrifiers. Organic carbon was fully removed, while phosphorus and nitrogen were not treated during the first 70 d. Zoogloea-like organisms can store soluble volatile fatty acids into intracellular polyhydroxyalcanoates (PHA). PHA-accumulating bacteria are expected to be denser and to settle faster than other species, and can stay in the AGS-SBR system during the initial washout dynamics. Zoogloea sp. can produce in addition extracellular polysaccharide polymers which could help to form and stabilize the early AGS biofilm structure.