Protein is an essential nutrient for sustaining human life; however, securing sufficient protein through the traditional livestock industry is predicted to become difficult in the future. Microalgae have high potential as alternative protein sources owing to their efficiency in resource utilization and sustainability. The major challenge in the high value-added use of microalgae is the effective recovery of their small cells. Electro-coagulation technology is a harvesting method that has little direct or indirect effect on microalgae and causes no environmental pollution. To optimize the harvest yield of Scenedesmus obliquus, this study examined how stirring, stirring speed, initial pH, electrode material, current density, current intensity, electrode spacing, and electrode placement affected microalgae recovery and determined optimal harvest conditions. The optimal culture conditions were a stirring speed of 100 rpm, initial pH of 5.0, using aluminum electrodes, current density of 20 A/m2, current intensity of 0.3 A, electrode spacing of 1 cm, and electrode placement of (–) electrode, (+) electrode, (–) electrode. These findings can be used to increase the harvest yield of microalgae as an alternative protein resource.