Granular sludge is a recent and attractive biological wastewater treatment process that relies on the formation of dense microbial aggregates. It offers excellent sludge settling abilities and allows a high biomass retention, which considerably reduces the capital and operational expenditures of treatment plants. In this thesis, we have explored new opportunities of improvement by combining microbiology and granulation strategies. In a first part, a biomass management strategy was developed to improve phosphate removal. This pollutant can be biologically removed from wastewaters by favoring the growth of phosphate-accumulating bacteria. By combining a low hydraulic selection pressure and a specific sludge discharge procedure, we achieved the selection of granules dominated by a population of Candidatus Accumulibacter with a high potential for phosphate accumulation, which resulted in excellent treatment performances. In a second part, we used granulation as a tool to inhibit the growth of filamentous bacteria, which are responsible for poor sludge settling and high loss of suspended solids. Starting from a highly filamentous sludge, an optimized reactor management procedure was elaborated to drive the microbial communities towards a well-settling granular biomass. The outcomes of this study were exported in a large full-scale plant treating dairy wastewaters and experiencing filamentous overgrowth. Shortly after setting the new strategy, the filaments disappeared and were replaced by granule-forming bacteria, which considerably improved the performances and reduced the energy consumption of the plant.