Microgrids have become an alternative for integrating distributed generation to supply energy to isolated communities, so their control and optimal management are important. This research designs and simulates the three levels of control of a DC microgrid operating in isolated mode and proposes an Energy Management System (EMS) based on Model Predictive Control (MPC), with real-time measurement feedback for optimal energy dispatch, which ensures power flow distribution and operation at minimum cost while extending the lifespan of the BESS. The EMS can react to disturbances produced in the lower control levels. The microgrid’s performance is analyzed and compared in two scenarios without EMS, and with EMS against changes in irradiation and changes in electricity demand. The fulfillment of the power balance is evaluated by analyzing the power delivered by each generation unit, the operating cost, and the state of charge of the battery (SOC).