Anoxic ammonium removal is limited by the lack of an electron acceptor. Six different microcosms were tested in parallel for a long-term operation. A constructed wetland-microbial fuel cell (CW-MFC) filled with manganese ore (MO) and activated carbon granules (AC) boosts the biochemistry of N-transformations under anoxic condition. The highest nitrogen removal was about 7.5 gN/(m2 d). With a COD/N = 1.7 in the influent, total nitrogen (TN) and chemical oxygen demand (COD) removal efficiencies of the coupling system increased by 53.5% and 29.6%, as compared with the control, respectively. Notably, the introduction of MO caused 891 ± 23 mV voltage output. The occurrence of different removal paths for ammonium in the presence of MO include adsorption, chemical oxidation and microbial nitrification. Altered extracellular polymeric substances (EPS) was involved in extracellular electron transfer (EET) processes and the cycle of Mn(Ⅳ)/Mn(Ⅱ) for accelerated nitrogen removal. The presence of AC expands the interaction between exoelectrogens and MO. Further study showed that Geobacter and Geothrix associated with electricity production and manganese reduction have been found generally in Mn-rich microcosms. This study provides valuable guidance for a removal of NH4+ under anoxic conditions and highlights the potential effect of triggering electron transfer for the development of energy production and pollutant remediation.