A structured metabolic model of the biological phosphorus removal process has been developed. In this approach the model is based on the bioenergetics and stoichiometry of the metabolism. All relevant metabolic reactions underlying the P-metabolism, considering also ATP and NADH2, are described. The derived set of stoichiometry based linear relations is used to reduce the number of reactions and conversions rates required to describe the process. The model predictions were experimentally verified by measurement of the external acetate, phosphate and ammonium concentrations as well as the internal fractions of PHB and glycogen. The model is applied to dynamic and steady-state situations over a wide range of sludge ages. The derived structured metabolic model is very well capable of describing the complex conversions of the biological phosphorus removal process.