The increasing use of distributed generators, which are mainly based on renewable sources, can create several issues in the operation of the electric grid. The microgrid is being analysed as a solution to the integration in the grid of the renewable sources at a high penetration level in a controlled way. The storage systems play a vital role in order to keep the energy and power balance of the microgrid. Due to the technical limitations of the currently available storage systems, it is necessary to use more than one storage technology to satisfy the requirements of the microgrid application. This work validates in simulations and experimentally the use of a Three-Level Neutral Point Clamped converter to control the power flow of a hybrid storage system formed by a SuperCapacitor and a Vanadium Redox Battery. The operation of the system is validated in two case studies in the experimental platform installed in ESTIA. The experimental results prove the validity of the proposed system as well as the designed control algorithm. The good agreement among experimental and simulation results also validates the simulation model, that can therefore be used to analyse the operation of the system in different case studies.