There is growing interest in recent times for microalgae as a sustainable energy source. However, efficient harvesting of microalgal biomass for various industrial applications is still considered a bottleneck. The present study attempts to evaluate microalgae Scenedesmus sp. harvesting using electro-coagulation-flocculation (ECF). Plackett-Burman design was exploited to explore the significant process parameters, whereas Taguchi's array design was employed for optimization. The optimal conditions were optimized as initial pH 5.0, electrolysis time 15 min, electrode distance 2 cm, sedimentation time 60 min, and current density 12 mA cm for complete harvesting. Under optimum conditions, the energy utilization and the operation cost of ECF process was estimated to be 2.65 kWh kg and USD 0.29 kg, respectively. Thus, ECF-based microalgae harvesting was found as a low-cost technique. In addition, neutralizing pH and supplementing macro- and micronutrients enabled the flocculated medium to maintain an approximate growth yield in algal cultivation to that of the fresh BG11 medium. ECF did not affect the amount of microalgal lipids (28.6 ± 1.2, % wt.), chlorophyll a (8.3 ± 0.3 μg mL), and fatty acid methyl ester composition (C15:0, C16:0, C17:0, and C18:0) as well. These results strongly recommend ECF as the most appropriate and promising method for harvesting Scenedesmus sp. for biofuel production.