A method and system for managing a battery system. The method including receiving at least one measured characteristic of the battery over a pre-defined time horizon from the at least one sensor, receiving at least one estimated characteristic of the battery from a electrochemical-based battery model based on differential algebraic equations, determining a cost function of a Moving Horizon Estimation based on the at least one measured characteristic and the at least one estimated characteristic, updating the electrochemical-based battery model based on the cost function, estimating at least one state of the at least one battery cell by applying the electrochemical-based battery model, and regulating at least one of charging or discharging of the battery based on the estimation of the at least one state of the at least one battery cell.