The aim of this study is to investigate conversion of nitrogen and COD in enriched paddy soil by nitrification coupled with anammox process in a dual chamber bioelectrochemical system. The paddy soil was enriched for denitrification coupled with anammox by microbial consortia and was acclimatized in the cathodic chamber of microbial fuel cells (MFCs). The bioelectrochemical systems were treated with different ammonium concentrations in the cathodic chamber: the MFC with low concentration ammonium (LA-MFC, 50 mg/L ammonium), the MFC with medium concentration ammonium (MA-MFC, 500 mg/L ammonium), and MFC with high concentration ammonium (HA-MFC, 1000 mg/L ammonium), and the initial COD in the anodic chamber was 1200 mg/L. The CK treatments were conducted with 1000 mg/L ammonium under the same conditions, except without inoculum in the cathode chamber. The consumption rate of ammonium in the cathodic chambers of CK, LA-MFC, MA-MFC, and HA-MFC were 9%, 64%, 84%, and 84%, respectively. The degradation rate for COD achieved in the anode chambers of CK, LA-MFC, MA-MFC, and HA-MFC were 70%, 86%, 93%, and 93%, respectively. The analysis of the microbial community of three treated MFCs in the cathode chamber indicated that the nitrification-denitrification process occurs in the cathode chamber. The dominant species for nitrification was Nitrospira, and the dominant species for denitrification were Denitratisoma, Dechloromonas, and Candidatus_Competibacter. Moreover, anammox process also observed in the cathode chamber. The functional genes nirS/K, hzsB, and 16S rDNA were assessed by qPCR analysis, and the results confirmed the presence of denitrification-coupled anammox in the cathodic chamber.