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This paper presents the mathematical formulation of the microgrid's energy management problem and its implementation in a centralized Energy Management System (EMS) for isolated microgrids. Using the model predictive control technique, the optimal operation of the microgrid is determined using an extended horizon of evaluation and recourse, which allows a proper dispatch of the energy storage units. The energy management problem is decomposed into Unit Commitment (UC) and Optimal Power Flow (OPF) problems in order to avoid a mixed-integer non-linear formulation. The microgrid is modeled as a three-phase unbalanced system with presence of both dispatchable and non-dispatchable distributed generation. The proposed EMS is tested in an isolated microgrid based on a CIGRE medium-voltage benchmark system. Results justify the need for detailed three-phase models of the microgrid in order to properly account for voltage limits and procure reactive power support.