Cyanobacterial blooms are a threat to the drinking water supply owing to their potential toxicity. Microcystins which are the most widespread cyanotoxins, are mainly produced by Microcystis spp. In this study, we cultured Microcystis aeruginosa cells in BG-11 medium at 25 °C to investigate the efficiency of the electro-coagulation–flotation process to remove them. Different anode materials (Fe, Al, Cu, and Zn) along with a graphite cathode were compared separately in the 10–100 mA current range in a 0.025 M Na2SO4 electrolyte. Turbidity, optical density at 684 nm (OD684), OD730, Chl-a concentration, and DOC concentration were analyzed to clarify the mechanism by which M. aeruginosa cells are removed. The Al anode indicated the highest removal efficiencies in terms of turbidity (90%), OD684 and OD730 (98%), and Chl-a concentration (96%) within 30 min at 4.0 mA/cm2 current density and the lowest average electrode consumption of 0.120 ± 0.023 g/L. The energy consumption of the Al electrode was 0.80 Wh/L. From these results, we found that Al was the best among the anode materials evaluated to remove M. aeruginosa cells. However, further studies are required to optimize the Al anode in terms of pH, treatment time, electrode distance, and electrolyte concentration to enhance the removal of M. aeruginosa cells.