Electrocoagulation (EC) is a facile technique for removing arsenic (As) pollutants from different water matrices with high efficiency. In this work, a novel strategy of Mn-assisted Fe EC was developed to further enhance the removal efficiency of arsenite [As(III)] from wastewater. When 1 mM of MnCl2 was added to an Fe-EC system, the As removal efficiency reached 99.99%, and the residual concentration was only 9 μg/L, which is lower than the World Health Organization’s limit for drinking water. The characteristics of the generated flocs by four different EC processes in Fe, Fe-Mn, Fe-As, and Fe-Mn-As systems were investigated. The results showed that Mn2+ promoted the formation of FeOOH, FeOx, MnOx, FeHAsO4, and MnHAsO4 through low crystallinity and a high surface area. Density functional theory simulation and crystal orbital hamiltonian population confirmed that the generated Fe-Mn flocs had a greater adsorption affinity for As(III) and arsenate [As(V)]. The possible reactions in the EC processes and reaction mechanisms were also hypothesised. The current work provides meaningful insights into understanding the mechanisms of Mn-assisted Fe-EC systems, and further confirms its potential for practical applications in As pollution treatment.