The performance of three solid oxide fuel cell (SOFC) systems, fuelled by biogas produced through anaerobic digestion (AD) process, for heat and electricity generation in wastewater treatment plants (WWTPs) is studied. Each system has a different fuel processing method to prevent carbon deposition over the anode catalyst under biogas fuelling. Anode gas recirculation (AGR), steam reforming (SR), and partial oxidation (POX) are the methods employed in systems I–III, respectively. A planar SOFC stack used in these systems is based on the anode-supported cells with Ni–YSZ anode, YSZ electrolyte and YSZ–LSM cathode, operated at 800 °C. A computer code has been developed for the simulation of the planar SOFC in cell, stack and system levels and applied for the performance prediction of the SOFC systems. The key operational parameters affecting the performance of the SOFC systems are identified. The effect of these parameters on the electrical and CHP efficiencies, the generated electricity and heat, the total exergy destruction, and the number of cells in SOFC stack of the systems are studied. The results show that among the SOFC systems investigated in this study, the AGR and SR fuel processor-based systems with electrical efficiency of 45.1% and 43%, respectively, are suitable to be applied in WWTPs. If the entire biogas produced in a WWTP is used in the AGR or SR fuel processor-based SOFC system, the electricity and heat required to operate the WWTP can be completely self-supplied and the extra electricity generated can be sold to the electrical grid.