This study compares the operation of mesophilic and thermophilic anaerobic digestion of sewage sludge and their effects in uncontrolled phosphorus precipitation. The research has been carried out using a pilot plant consisting of two digesters of 1.6 m3 working volume, treating the mixed sludge of Alzira WWTP (Valencia, Spain). The digesters were operated in parallel, at different conditions: mesophilic (38 ± 2.0°C) and thermophilic (55 ± 2.5°C) temperatures and organic loading rates (OLR) ranging from 1.1 to 1.7 kg volatile solids (VS) m−3 d−1 and different hydraulic retention times (HRT) 20, 15 and 12 days. Uncontrolled precipitation was evaluated through P, Mg and Ca mass balances in both digesters. The results revealed that up to 82% of the available P and 81% of the available Mg precipitated in the mesophilic digester at HRT = 20 days which suggests the possible formation of struvite in both digesters. At lower HRT (HRT = 12 days) Mg and Ca precipitation was negligible and P fixation has been attributed to the possible formation of iron phosphates or adsorption processes on solid surfaces.