This paper proposes a method that leads to a highly accurate state-of-charge dependent multi-stage constant current (MCC) charging algorithm for electric bicycle batteries to reduce the charging time without accelerating aging by avoiding Li-plating. First, the relation between the current rate, state-of-charge, and Li-plating is experimentally analyzed with the help of three-electrode measurements. Therefore, a SOC-dependent charging algorithm is proposed. Secondly, a SOC estimation algorithm based on an Extended Kalman Filter is developed in MATLAB/Simulink to conduct high accuracy SOC estimations and control precisely the charging algorithm. The results of the experiments showed that the Root Mean Square Error (RMSE) of SOC estimation is 1.08%, and the charging time from 0% to 80% SOC is reduced by 30%.