This paper presents a complete control scheme to efficiently manage the operation of an autonomous wind based hydrogen production system. This system comprises a wind energy generation module based on a multipolar permanent magnet synchronous generator, a lead-acid battery bank as short term energy storage and an alkaline von Hoerner electrolyzer. The control is developed in two hierarchical levels. The higher control level or supervisor control determines the general operation strategy for the whole system according to the wind conditions and the state of charge of the battery bank. On the other hand, the lower control level includes the individual controllers that regulate the respective module operation assuming the set-points determined by the supervisor control. These last controllers are approached using second-order super-twisting sliding mode techniques. The performance of the closed-loop system is assessed through representative computer simulations.