An iron‐nitrogen‐carbon‐based catalyst was used at the cathode of a microbial desalination cell (MDC) and compared with platinum (Pt) and an activated carbon (AC) cathode. The Fe‐N−C catalyst was prepared by using nicarbazin (NCB) as the organic precursor through a sacrificial support method (SSM). Rotating ring disk electrode (RRDE) experiments show that Fe‐NCB had a higher electrocatalytic activity compared to AC and Pt. The utilization of Fe‐NCB in the cathode substantially improved the performance output with an initial maximum power density of 49±2 μW cm−2 in contrast to Pt and AC catalysts, which show lower values of 34±1 and 23.5±1.5 μW cm−2, respectively. After four cycles, Fe‐NCB catalyst lost 15 % of its initial performance, but still was 1.3 and 1.8 times more active than Pt and AC, respectively. Solution conductivity inside the desalination chamber (DC) decreased by 46–55 % with every cycle. The pH of the cathodic chamber and the DC increased to 10–11, owing to the production of OH− during the oxygen reduction reaction and the migration of OH− into the DC. Chemical organic demand decreased by 73–83 % during each cycle. It was shown that Fe‐NCB and Pt had a similar coulombic efficiency (CE) of 39±7 % and 38±2 %, whereas AC had lower CE (24±5 %).