Increasing demand for distributed generation based on Renewable Energy Sources (RES) has led to several issues in the operation of utility grids. The micro grid is a hopeful solution to solve these problems. A dedicated energy storage system could contribute to a better integration of RES into the micro grid by smoothing the renewable resource’s intermittency, improving the quality of the injected power and enabling additional services like voltage and frequency regulation. However, due to energy/power technological limitations, it is often necessary to use Hybrid Energy Storage Systems (HESS). In this paper, a second order sliding mode controller is proposed for the power flow control of a HESS, using a Four Leg Three Level Neutral Point Clamped (4-Leg 3LNPC) inverter as the only interface between the RES/HESS and the micro grid. A three-dimensional space vector modulation and a sequence decomposition based AC side control allows the inverter to work in unbalanced load conditions while maintaining a balanced AC voltage at the point of common coupling. DC current harmonics caused by unbalanced load and the NPC floating middle point voltage, together with the power division limits are carefully addressed in this paper. The effectiveness of the proposed technique for the HESS power flow control is compared to a classical PI control scheme and is proven through simulations and experimentally using a 4 Leg 3LNPC prototype on a test bench.