The novel aerobic granular sludge technology is attractive for intensified biological nutrient removal from wastewater. This process is based on self-granulated flocs forming fast-settling mobile biofilms with a gel-like consistence, called “granules”. Mechanisms of bacterial selection and self-immobilisation as spherical biofilms have risen fundamental interest. Investigations were conducted on the relationship between the bacterial populations involved and the resulting internal granular architectures. Bacterial and structural dynamics from flocs to granules were followed in anaerobic-aerobic sequencing batch reactors operated under different conditions selecting for fast-growing heterotrophic organisms (floc-forming Zoogloea and filamentous Burkholderiales affiliates), for slower-growing polyphosphate-accumulating organisms (“Ca. Accumulibacter”) and their glycogen-accumulating competitors (“Ca. Competibacter”), as well as for nitrifying organisms. Dynamics of bacterial community compositions were analyzed using a novel PyroTRF-ID bioinformatics methodology combining T-RFLP and pyrosequencing targeting the 16S rRNA gene pool. Structural times series were followed by CLSM combined with overall biomass staining with Rhodamine 6G, with fluorescence lectin-binding analysis (FLBA) of glycoconjugate matrices, and with 16S rRNA targeted FISH to monitor the spatial dynamics of phylotypes within granules. Under wash-out conditions, initial predominance of fast-growing Zoogloea spp. resulted in the formation of smooth and homogeneous granular biofilms by swelling and outgrowth of Zoogloea colonies around flocs. These continuous zoogloeal biofilm matrices were then embedding the proliferation of dense clusters of Accumulibacter, Competibacter, and nitrifiers from the granule core outwards. This led to the formation of heterogeneous multispecies mature granular biofilms. Granules cultivated in enrichment cultures of Accumulibacter and Competibacter resulted from the heterogeneous development of compact microcolonies around flocs. Under unfavorable conditions, filamentous Burkholderiales structures proliferated by penetrating outside granules leading to impaired settling performances. In conclusion, biofilm granulation mechanisms depend on the predominant organisms involved, and on their physiological properties. According to FLBA, the structural gelling agent is likely to exhibit a complex exopolysaccharide composition.