The aim of this study was to improve phosphorus removal in aerobic granular sludge sequential batch reactors (AGS-SBR) by a differential selection of the granules containing the highest proportion of phosphate accumulating organisms (PAOs). The abundance of PAOs in granules with different density was analyzed by PCR-DGGE, pyrosequencing and qPCR. Dense granules contained a higher proportion of Candidatus Accumulibacter (PAO) with a 16S rRNA gene frequency up to 45%, corresponding to 6.8 log PAO-specific 16S rRNA gene copies per ng DNA. A further distinction was proposed between dense and very dense granules, the latter maintaining a lower population of Ca. Accumulibacter. Starting with and AGS-SBR with low heigh/diameter ratio performing unstable P removal, two strategies of biomass removal were assessed. First, a high selective pressure (short settling time) was applied to discharge excess solids with the effluent and second, an increase of the settling time was combined with a homogeneous purge of the sludge bed. The first strategy resulted in a reduction of P removal efficiency while the second improved and stabilized P removal over 90%. It resulted in a shift in bacterial populations and a decrease of the bacterial diversity. This study offers a new approach of biomass management to further improve phosphorus removal in sequencing batch reactors.