The present invention discloses a twin chamber upflow bio-electrochemical reactor (TCUBER). The bio-electrochemical reactor was designed to consist of two columns joined together by a cation permeable membrane connection. These two columns are functioned as the anode and cathode chambers and to provide the desired oxic and anoxic conditions for microorganisms by passing the electric current through these two columns. Palm shell granular activated carbon (PSGAC) was packed into both columns as biocarrier of the microorganisms and third electrode during the nitrification and denitrification process.