The growth of the world’s energy demand over recent decades in relation to energy intensity and demography is clear. At the same time, the use of renewable energy sources is pursued to address decarbonization targets, but the stochasticity of renewable energy systems produces an increasing need for management systems to supply such energy volume while guaranteeing, at the same time, the security and reliability of the microgrids. Locally distributed energy storage systems (ESS) may provide the capacity to temporarily decouple production and demand. In this sense, the most implemented ESS in local energy districts are small–medium-scale electrochemical batteries. However, hydrogen systems are viable for storing larger energy quantities thanks to its intrinsic high mass-energy density. To match generation, demand and storage, energy management systems (EMSs) become crucial. This paper compares two strategies for an energy management system based on hydrogen-priority vs. battery-priority for the operation of a hybrid renewable microgrid. The overall performance of the two mentioned strategies is compared in the long-term operation via a set of evaluation parameters defined by the unmet load, storage efficiency, operating hours and cumulative energy. The results show that the hydrogen-priority strategy allows the microgrid to be led towards island operation because it saves a higher amount of energy, while the battery-priority strategy reduces the energy efficiency in the storage round trip. The main contribution of this work lies in the demonstration that conventional EMS for microgrids’ operation based on battery-priority strategy should turn into hydrogen-priority to keep the reliability and independence of the microgrid in the long-term operation.