Chlorella vulgaris, one of the single cell protein sources, is a promising alternative to address the ever-growing demand for food-quality protein. Efforts have been made to overcome the high production costs by using wastewater for the cultivation of C. vulgaris. However, direct use of wastewater poses threats to the safety of applying the obtained biomass for food and animal feed. This study applied a novel three-chamber microalgal-bio-electrochemical systems for simultaneous clean cultivation of C. vulgaris and treatment of industrial organic wastewater. Results demonstrated that the removal of COD (38.7–66.8%) and total Kjeldahl nitrogen (TKN, 49.8–69.0%) improved with the increase of electric current in both anode and cathode chambers. Meanwhile, comparable phosphorus removal rates of 34.2–48.5% were achieved in all operation modes. Through nutrients migration, the middle chamber recovered 34.4–39.4% TKN, 16.8–47.3% phosphorus, and acetate from the wastewater to support a mixotrophic growth of C. vulgaris. Moreover, increasing electric current promoted higher dry algal biomass weight (0.87–1.11 g L−1), higher protein content (320.8–552.1 mg Protein g−1 Biomass), and larger cell size (enlarged up to 151.2%) than the control. Nevertheless, the ratio of protein content decreased with the increase of cell size due to the prior accumulation of other compounds under mixotrophic growth. This study provides a sustainable approach for the conversion from industrial organic wastewater to clean production of microalgal protein.