In this work, benzimidazole (BZIM) and aminobenzimidazole (ABZIM) were used as organic-rich in nitrogen precursors during the synthesis of iron-nitrogen-carbon (Fe-N-C) based catalysts by sacrificial support method (SSM) technique. The catalysts obtained, denoted Fe-ABZIM and Fe-BZIM, were characterized morphologically and chemically through SEM, TEM, and XPS. Moreover, these catalysts were initially tested in rotating ring disk electrode (RRDE) configuration, resulting in similar high electrocatalytic activity toward oxygen reduction reaction (ORR) having low hydrogen peroxide generated (<3%). The ORR performance was significantly higher compared to activated carbon (AC) that was the control. The catalysts were then integrated into air-breathing (AB) and gas diffusion layer (GDL) cathode electrode and tested in operating microbial fuel cells (MFCs). The presence of Fe-N-C catalysts boosted the power output compared to AC cathode MFC. The AB-type cathode outperformed the GDL type cathode probably because of reduced catalyst layer flooding. The highest performance obtained in this work was 162 ± 3 μWcm-2. Fe-ABZIM and Fe-BZIM had similar performance when incorporated to the same type of cathode configuration. Long-term operations show a decrease up to 50% of the performance in two months operations. Despite the power output decrease, the Fe-BZIM/Fe-ABZIM catalysts gave a significant advantage in fuel cell performance compared to the bare AC.