Bioelectrochemical systems are emerging as a promising and friendly alternative to convert the energy stored in wastewater directly into electricity by microorganisms and utilize it in situ to drive desalination. To better understand such based-processes, we propose the development of an Anoxic Biocathode Microbial Desalination Cells for the conversion of carbon and nitrate rich-wastewaters into bioenergy and perform salt removal. Our results demonstrate a power output of 0.425 W m−3 with desalination, organic matter removal and nitrate conversion efficiencies of 43.69%, 99.85% and 92.11% respectively. Microbiological analysis revealed Proteobacteria as dominant Phyla in the anode (88.45%) and biocathode (97.13%). While a relative higher bacterial abundance was developed in the anode chamber, the biocathode showed more selected microorganisms, with a predominance of Paracoccus (73.2%), which are related to the denitrification process. These findings are promising and provide new opportunities for the development and application of this technology in the field of wastewater treatment to produce cleaner water and conservating natural resources.