Energy systems are experiencing rapid change, exemplified by the increasing use of power electronics and distributed generation units along with their fast and potentially unstable dynamics. To ensure the optimal coordination of these components, we propose a distributed secondary control based on MPC strategies which exploits the flexibility provided by underlying passivity-based primary controllers. Using DC microgrids as an example, we derive a separable and topology-independent Lyapunov function together with independent terminal constraints for ensuring stability of the MPC controller. We also contrast classical tracking and economic MPC implementations, and demonstrate the improved performance achieved by the latter when disturbances occur. Lastly, we argue that the proposed methodology is readily applicable to other energy system domains equipped with passivity-based controllers.