This work analyses the use of a Three-Level Neutral Point Clamped (3LNPC) converter to control the power flow of a Hybrid Energy Storage System (HESS) and at the same time interconnect it with the common AC bus of a microgrid. Nowadays there is not any storage technology capable of offering a high energy storage capacity, a high power capacity and a fast response at the same time. Therefore, the necessity of hybridising more than one storage technology is a widely accepted idea in order to satisfy the mentioned requirements. This work shows how the operational limits of the 3LNPC converter can be calculated and integrated in a control structure to facilitate an optimal use of the HESS according to the rules fixed by the user.