Enhanced biological phosphorus removal (EBPR) is usually limited by organic carbon availability in wastewater treatment plants (WWTPs). Polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs) were operated under extended periods with low organic carbon loading in order to examine its impact on their activity and survival. The decrease in organic carbon load affected PAOs and GAOs in different ways, where the biomass decay rate of GAOs was approximately 4 times higher than PAOs. PAOs tended to conserve a relatively high residual concentration of polyhydroxyalkanoates (PHAs) under aerobic conditions, while GAOs tended to deplete their available PHA more rapidly. This slower oxidation rate of PHA by PAOs at residual concentration levels enabled them to maintain an energy source for aerobic maintenance processes for longer than GAOs. This may provide PAOs with an advantage over GAOs in surviving the low organic loading conditions commonly found in full-scale wastewater treatment plants.