In wastewater treatment plants (WWTPs), aeration is the major energetic cost, thus its minimisation will improve the cost-effectiveness of the process. This study shows that both the dissolved oxygen (DO) concentration and aerobic hydraulic retention time (HRT) affect the competition between polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs). At low DO levels, Accumulibacter PAOs were shown to have an advantage over Competibacter GAOs, as PAOs had a higher oxygen affinity and thus largely maintained their aerobic activity at low DO levels, while GAO activity decreased. Bioreactor operation at low DO levels was found to increase the PAO fraction of the sludge. Furthermore, an increase in aerobic HRT (at a DO level of 2 mg O2/L), promoted the proliferation of GAOs over PAOs, decreasing the EBPR efficiency. Overall, this study shows that low aeration can be beneficial for EBPR performance through selecting for PAOs over GAOs, which should be incorporated into WWTP models in order to minimise energetic costs and improve WWTP sustainability.