A high penetration of the Renewable Energy Sources (RES) can create stability, reliability and power quality problems in the main electrical grid due to their stochastic nature. The microgrid is one of the analysed solutions to solve this problem. In this context, the storage becomes necessary to better harness the energy generated by RES and to maintain the proper operation of the microgrid. This paper addresses the control of the bidirectional DC-DC converters used to interface a parallel connected Hybrid Energy Storage System (HESS) formed by a Vanadium Redox Battery (VRB) and a SuperCapacitor (SC) bank. The linear controllers have been widely used due to their simple design and implementation. However, their operation is limited to a certain operation range. The variability of the analysed system makes the use of a more robust controller necessary. In this work a PI based two-loop control system and a PI type sliding mode controller (SMC) are compared by means of simulations using the Matlab-Simulink software. Some rules are fixed to facilitate the design process of the SMC and the advantages of using a nonlinear controller are stressed.