In many biological wastewater treatment systems, bacterial growth and the amount of active biomass are limited by the availability of substrate. Under these low growth conditions, endogenous processes have a significant influence on the amount of active biomass and therefore, the overall system performance. In enhanced biological phosphorus removal (EBPR) systems endogenous processes can also influence the levels of the internal storage compounds of the polyphosphate accumulating organisms (PAO), directly affecting phosphorus removal performance. The purpose of this study was to evaluate the significance of different endogenous processes that occur during the long-term starvation of EBPR sludge under aerobic and anaerobic conditions. Activated sludge obtained from a laboratory sequencing batch reactor was used to perform a series of batch starvation experiments. Under aerobic starvation conditions we observed a significant decay of PAO (first-order decay rate of 0.15/d) together with a rapid utilization of polyhydroxyalkanoates (PHA) and a slower utilization of glycogen and polyphosphate to generate maintenance energy. On the other hand, anaerobic starvation was best described by maintenance processes that rapidly reduce the levels of polyphosphate and glycogen under starvation conditions while no significant decay of PAO was observed. The endogenous utilization of glycogen for maintenance purposes is currently not included in available EBPR models. Our experimental results suggest that mathematical models for in EBPR should differentiate between aerobic and anaerobic endogenous processes, as they influence active biomass and storage products differently.