This paper presents a novel energy management strategy (EMS) to control a wind-hydrogen microgrid which includes a wind turbine paired with a hydrogen-based energy storage system (HESS), i.e., hydrogen production, storage and re-electrification facilities, and a local load. This complies with the mini-grid use case as per the IEA-HIA Task 24 Final Report, where three different use cases and configurations of wind farms paired with HESS are proposed in order to promote the integration of wind energy into the grid. Hydrogen production surpluses by wind generation are stored and used to provide a demand-side management solution for energy supply to the local and contractual loads, both in the grid-islanded and connected modes, with corresponding different control objectives. The EMS is based on a hierarchical model predictive control (MPC) in which long-term and short-term operations are addressed. The long-term operations are managed by a high-level MPC, in which power production by wind generation and load demand forecasts are considered in combination with day-ahead market participation. Accordingly, the hydrogen production and re-electrification are scheduled so as to jointly track the load demand, maximize the revenue through electricity market participation and minimize the HESS operating costs. Instead, the management of the short-term operations is entrusted to a low-level MPC, which compensates for any deviations of the actual conditions from the forecasts and refines the power production so as to address the real-time market participation and the short time-scale equipment dynamics and constraints. Both levels also take into account operation requirements and devices’ operating ranges through appropriate constraints. The mathematical modeling relies on the mixed-logic dynamic (MLD) framework so that the various logic states and corresponding continuous dynamics of the HESS are considered. This results in a mixed-integer linear program which is solved numerically. The effectiveness of the controller is analyzed by simulations which are carried out using wind forecasts and spot prices of a wind farm in center-south of Italy.