Agro-industry wastewaters normally contain high levels of organic matter and require suitable treatment before discharge. The use of Microbial fuel cells, a novel wastewater treatment, can provide advantages over existing treatment methods. In this study, an up-flow bio-filter circuit (UBFC) for treating wastewaters without chemical treatment or nutrient supplement, was developed to solve a clogging problem. The optimal conditions included an organic loading rate of 30.0 g COD/L-d, hydraulic retention time of 1.04 day, pH level of 5.6-6.5 and aeration at 2.0 L/min. External resistance of the circuit was tested. COD removal levels of 8.08, 20.1 and 26.67 g COD/L-d were obtained, while fed with sea food, biodiesel and palm oil mill wastewater, respectively. These rates are higher than for conventional technologies. The carbon fiber brush immobilized base increased the performance of the new UBFC by 17.54% over that obtained in a previous study, while the cost was slightly decreased about 4.48%.