This paper proposes a multi-objective model predictive control (MPC) designed for the power management of a multi-stack fuel cell (FC) system integrated into a renewable sources-based microgrid. The main advantage of MPC is the fact that it allows the current timeslot to be optimized while taking future timeslots into account. The multi-objective function solves the problem related to the power dispatch at time that includes criteria to reduce the multi-stack FC degradation, operating and maintenance costs, as well as hydrogen consumption. Regarding the scientific literature, the novelty of this paper lies in the proposal of a generalized MPC controller for a multi-stack FC that can be used independently of the number of stacks that make it up. Although all the stacks that make up the modular FC system are identical, their levels of degradation, in general, will not be. Thus, over time, each stack can present a different behavior. Therefore, the power control strategy cannot be based on an equal distribution according to the nominal power of each stack. On the contrary, the control algorithm should take advantage of the characteristics of the multi-stack FC concept, distributing operation across all the stacks regarding their capacity to produce power/energy, and optimizing the overall performance.