The aim of this paper is to study the microbial and structural changes occurring during the transition from flocculent (used as inoculum) to biofilm and granular sludge in a Sequencing Batch Biofilter Granular Reactor (SBBGR). SBBGR is a new and promising technology characterised by low sludge production (5-6 times lower than in conventional treatment plants), high biomass concentration (up to 35 g TSS/L(bed)), high COD conversion capacity, high effluent quality and operation flexibility. Molecular in situ detection methods and microscopy staining procedures were employed in combination with the traditional measurements (i.e., oxygen uptake rate, COD removal efficiency) to evaluate the microbial activity and composition of the granular biomass. The granules structure was investigated by electron scanning microscopy, phase contrast analysis of granule sections and specific extracellular polymeric substances (EPS) stainings. Evident changes in biomass composition was observed during the shift from activated to granular sludge while a stable presence of active bacterial populations (mainly Proteobacteria) was found within mature granules.