Aerobic granules are quasi-spherical biofilms mainly composed of self-immobilized mixed microbial communities. The application of aerobic granules to treat domestic and low-strength industrial wastewaters is gaining attention because granules can accommodate high biomass concentrations and this translates into small foot-print treatment reactors. For robust application of this novel treatment technology, aerobic granules should be physically stable, and to account for the removal of the desired contaminants, should contain an appropriate microbial assembly. One main challenge is to engineer and control the granules microbial assembly. This requires a good understanding of the microbial composition and dynamics in relation to process parameters and process performance; and the incorporation of this knowledge as feedback tool for optimized reactors operation. For the removal of phosphorus, phosphate accumulating organisms (PAO) are crucial players. Hence their abundance is desirable and the recognition of key operational parameters that guarantee their population stability is important. In this study we developed aerobic granules using two different carbon sources and through this process we determined their microbial composition and dynamics and its association to reactor functionality. To assess temporal changes in bacterial and in PAO community structures, 16S rRNA gene- and polyphosphate kinase (ppk1) gene-based community fingerprint patterns were assessed via terminal restriction fragment length polymorphism (T-RFLP), respectively. Analysis of the community dynamics showed that during granules development, the microbial richness dropped considerably suggesting that granulation is a very selective process. Propionate favored the establishment of PAO populations as compared to acetate. Based on ppk1 gene community fingerprint analysis, the carbon source selected for different PAO strains in the two systems and resulted in an excellent phosphorus removal capacity in the propionate fed reactor while phosphorus removal upsets were observed in the acetate fed reactor despite the presence of PAO.