The world is predicted to face serious threats from the depletion of non-renewable energy resources, freshwater shortage, and food scarcity. Microbial fuel cells (MFCs) are innovative bio-electrochemical devices capable of directly converting chemical energy into electrical energy using microorganisms as a catalyst. This ability has been explored for generating electricity using wastewater as an energy source, while simultaneously treating wastewater. On the other hand, hydroponics is the cultivation of plants in water without soil. The goal of this study was to develop a novel integrated microbial fuel cell-hydroponic system (MFC-Hyp system) that possesses the ability to concurrently generate electricity while degrading organic pollutants (Chemical oxygen demand, COD) in wastewater, remove and recover nutrients (phosphorus, P and nitrogen, N) from the wastewater, and produce edible plants. The MFC-Hyp system developed in this study produced a power density of 250.7 mW/m2. The power density increased by approximately 19% and the phosphorus recovery increased to 7.5% in the presence of Allium tuberosum compared to 4.9% without the plant (e.g., in the control). The removal efficiencies of nitrate, phosphate, and COD are 32%, 11%, and 80%, respectively. The results indicate that the novel integrated MFC-Hyp system can remove COD from wastewater, generate electricity using wastewater as an energy source, and utilize nutrients for growing plants; however, this system requires further improvement for field implementation.