In the present work, sludge from a stable and efficient phosphorus removal process was used to evaluate the change in the metabolism when the reactor operation was modified from anaerobic/aerobic to aerobic dynamic substrate feeding. The change in operational conditions allowed the population to modify the metabolism of phosphorus and polyhydroxyalkanoates (PHA) accumulation. Under aerobic dynamic feeding, phosphorus accumulation was almost hindered while the amount of PHA accumulation increased significantly. After ten days of operation under dynamic substrate feeding, the reactor operation turned back to anaerobic/aerobic cycles and the metabolism of phosphorus was progressively recovered.