The aim of this paper is to study the precipitation process in a sequencing batch reactor (SBR) operated for EBPR (enhanced biological phosphorus removal) and the possible effects of this phosphorus precipitation in the biological process. Four experiments were carried out under different influent calcium concentration. The experimental results and the equilibrium study, based on the Saturation Index calculation, confirm that the process controlling the calcium behaviour in a SBR operated for EBPR is the calcium phosphate precipitation. This precipitation takes place at two stages initially precipitation of the ACP and later crystallization of HAP. Also the accumulation of phosphorus precipitated was observed when the influent Ca concentration was increased. In all the experiments the influent wastewater ratio P/COD was kept constant. It has been observed that at high Ca concentration the amount of poly-P granules decrease, decreasing the ratio between phosphate release and acetate uptake (Prel/Acuptake). Changes on PAO and GAO populations during the experimental period were ruled out by means of methilene blue stains for poly-P detection. These results confirmed the phosphate precipitation as a process that can affect to the PAO metabolism and the EBPR performance.