Enhanced biological phosphorus removal by anaerobic-aerobic operation is not always achieved successfully. In this study, microbial metabolism in the activated sludge of a failed enhanced biological phosphorus removal process was investigated to clarify the cause of the failure. The dominant microorganisms in the sludge consumed carbohydrates in the uptake process of acetate or propionate under anaerobic conditions and accumulated polyhydroxyalkanaate. But significant release of phosphate was not observed because polyphosphate was not utilized. Consumed carbohydrates were found to have been converted to polyhydroxyalkanoate via propionyl-CoA in addition to acetyl-CoA, indicating that the microorganisms had enzymes to convert phosphoenolpyruvate or pyruvate produced in glycolysis to propionyl-CoA. The propionate fermentation was supposed to work as the sink of the reducing power excessively produced in glycolysis; thus while maintaining the redox balance, microorganisms were able to get energy not from polyphosphate but from glycogen. The difference in the metabolic systems between polyphosphate accumulating bacteria and the present microorganisms may give hints to avoid the deterioration of enhanced biological phosphorus removal.