Microgrids have become valuable assets because they improve the reliability of consumers while integrating renewables via distributed energy resources (DERs). Thus, making them cost-efficient is essential to secure their proliferation. This paper proposes a new method for the optimal design of microgrids. The proposed two-stage method optimizes the size and the location of the DERs, i.e., the renewable energy sources (RESs), distributed generation (DG) units, and battery energy storage systems (BESSs). Furthermore, the overall operation of the microgrid is optimized using a stochastic scenario-based approach, considering grid-connected and unintentional islanded modes. The proposed method also considers internal network reinforcements. Thus, the first stage is an energy-based approach, formulated as a mixed-integer linear programming (MILP) problem, and it is used to size the DERs, whereas the second stage uses an optimal AC power flow (AC-OPF) to formulate a mixed-integer nonlinear programming (MINLP) model that allocates the DERs and selects the best conductor for each circuit. The multi-objective nature of the problem is addressed via Pareto optimization to analyze the trade-off between operational and capital costs. The MINLP model is linearized through piece-wise approximations and solved using commercial solvers. Furthermore, the impact of battery degradation is analyzed through a simple adaptation of the Stage 1 model. Results were obtained with data from the real university campus microgrid CampusGrid, located at the State University of Campinas (UNICAMP), in São Paulo, Brazil.