The Murcia Este Wastewater Treatment Plant is the largest wastewater treatment plant in Murcia (Spain). The plant operators have continuously found pipe blockage and accumulation of solids on equipment surfaces during the anaerobic digestion and post-digestion processes. This work studies the precipitation problems in the Murcia Este Wastewater Treatment Plant in order to locate the sources of precipitation and its causes from an exhaustive mass balance analysis. The DAF thickener and anaerobic digester mass balances suggest that most of the polyphosphate is released during excess sludge thickening. Despite the high concentrations achieved in the thickened sludge, precipitation does not occur at this point due to the low pH. The increases in ammonium and pH during anaerobic digestion cause precipitation to take place mainly inside the digesters and in downstream processes. This study shows that 50.7% of the available phosphate is fixed in the digester of which 52.0% precipitates as ammonium struvite, 39.2% precipitates as hydroxyapatite and the remaining 8.8% is adsorbed on the surface of the solids. Thermodynamic calculations confirm the precipitation of struvite and hydroxyapatite and also confirm that potassium struvite does not precipitate in the anaerobic digesters.