A laboratory-scale granular sequencing batch reactor, fed with acetate, was operated at two different ratios of chemical oxygen demand to phosphorus-15:1 and 100:1. Smaller aerobic granules, but with better settleability, were obtained at the lower ratio. High ratio of phosphorus release to uptake of dissolved organic carbon (0.42 mol/mol) coincided with high percentage of polyphosphate-accumulating organisms (up to 70 % of all bacteria) and implied high metabolic activity of these bacteria. Polyphosphate-accumulating organisms belonged mainly to Accumulibacter and Tetrasphaera (46 and 23 %, respectively). Despite significant abundance, Tetrasphaera-related microorganisms were not detected by oligoprobes Actino-221 and Actino-658, but by broader oligoprobes Tet2-892 and Tet3-654. Low abundance (1 %) of Halomonas phosphatis indicated a minor role of these bacteria in the laboratory-scale reactor fed with synthetic wastewater. When the ratio of chemical oxygen demand to phosphorus was increased to 100:1, deterioration of settling properties was observed, caused by growth of filamentous organisms from Thiothrix/021N group. The higher ratio favoured Competibacter and was selected against all groups of polyphosphate-accumulating organisms. However, a significant percentage (10 %) of polyphosphate-accumulating organisms in the granular sludge with concomitant low ratio of phosphorus release to the uptake of dissolved organic carbon (0.01 mol/mol) suggested shift in the overall population metabolism. Under phosphorus limitation in wastewater, polyphosphate-accumulating organisms no longer synthesized poly-P and behaved as glycogen-accumulating organisms.