This article presents a decentralized control strategy applied to a multi-source power system having a fuel cell (FC) system as a main power source and a secondary storage element (SSE) for peak current supply during transients and energy recovery during braking. The dedicated control structure aims to assure an optimal operation of the FC system and a desired energy level of the SSE. To attain these objectives, a dynamic model of the FC system (stack and auxiliary devices necessary to fuel cell operation) is used, in addition to the SSE dynamics. The FC system regulation and the control of the SSE state of energy are performed separately with two different controllers, both designed using a model predictive control (MPC) approach. A first controller is employed in order to ensure a high efficiency of the FC system while respecting the compressor physical limits (limited voltage of the compressor motor, bounded operation region). The performances of the MPC strategy are evaluated in simulation and compared to the ones of a classic PID regulator. A second controller is used to obtain a desired SSE charge level for a given load profile, by guaranteeing a positive FC current and a bounded state of energy. The decentralized control approach proposed for this multivariable system allows to reduce the computational complexity, compared to a centralized approach. The validation of the control structure is performed in simulation using a nonlinear model of the FC system.