This work deals with the prediction of variables for a hydrogen energy storage system integrated into a microgrid. Due to the fact that this kind of system has a nonlinear behaviour, the use of traditional techniques is not accurate enough to generate good models of the system under study. Then, a hybrid intelligent system, based on clustering and regression techniques, has been developed and implemented to predict the power, the hydrogen level and the hydrogen system degradation. In this research, a hybrid intelligent model was created and validated over a dataset from a lab-size migrogrid. The achieved results show a better performance than other well-known classical regression methods, allowing us to predict the hydrogen consumption/generation with a mean absolute error of 0.63% with the test dataset respect to the maximum power of the system.