Biogas from anaerobic digestion of organic matter is a promising renewable energy source and fuel cells appear as a breakthrough technology to improve the performance of the biogas-to-energy valorisation chain. The vast majority of studies addressing biogas energy recovery through Solid Oxide Fuel Cells published in recent years correspond to simulations and lab-scale performance with synthetic biogas. This paper assesses the pilot performance of a 2.8 kWe SOFC unit powered with cleaned sewage biogas for around 700 h in a Wastewater Treatment Plant. The biogas thorough treatment consisting of a biological desulphurisation with a biotrickling filter followed by a deep cleaning step based on adsorption is successful for removing sulphur compounds, siloxanes and hydrocarbons. The influence of the heat-to-power ratio on fuel cell performance is investigated operating the system at O/C ratio of 2, reforming temperature of 550 °C, stack temperature of 800 °C and at a constant voltage of 43 V. At optimized conditions for electrical production satisfying heat demand in the WWTP, system electrical and thermal efficiencies account for 34% and 28%. Cogeneration efficiency remains constant at around 59–62% for all the heat-to-power ratios tested. Furthermore, the impact of the oxygen content in the biogas is also studied