This paper proposes a bilevel formulation for a coupled planning and operation problem of an advanced microgrid. The proposed model, recast as a mathematical program with equilibrium constraints (MPEC), determines jointly the optimal configuration of the microgrid, while optimizing the output of the distributed energy resources (DER) through the implementation of an energy management system (EMS). The approach further analyzes the available investment options for the microgrid using capital budgeting techniques to determine the return on investment to various microgrid stakeholders. The proposed approach was applied to the energy infrastructure of an off-grid mine. Results obtained through its application show significant savings in the cost of energy and improved benefits to stakeholders.