Aerobic granular sludge is a biological wastewater treatment process in which a microbial community forms a granular biofilm. The role of Candidatus Accumulibacter in the production of a biofilm matrix, composed of extracellular polymeric substances, was studied in a sequencing batch reactor enriched with polyphosphate-accumulating organisms. The metabolisms of the microbial populations were investigated using de novo metatranscriptomics analysis. Finally, the effect of decreasing the influent phosphate concentration on the granule stability and microbial activity was investigated. A few weeks after the reactor start-up, the microbial community was dominated by Accumulibacter with up to nine species active in parallel. However, the most active species differed according to sampling time. Decreasing drastically the influent phosphate concentration led to a dominance of the glycogen-accumulating organism Propionivibrio, with some Accumulibacter species still abundant. De novo metatranscriptomics analysis indicated a high diversity of potential extracellular substances produced mainly by Accumulibacter, Azonexus, Candidatus Contendobacter, and Propionivibrio. Moreover, the results suggest that Azonexus, Contendobacter and Propionivibrio recycle the neuraminic acids produced by Accumulibacter. Changes in the microbial community did not cause the granules to disintegrate, indicating that a Propionivibrio-dominated community can maintain stable granules.