This paper focuses on applying multicriteria decision making tools to determine an optimal energy retrofit plan for a portfolio of buildings. We present a two-step decision making technique employing a multiobjective optimization algorithm followed by a multiattribute ranking procedure. The method aims at deciding, in an integrated way, the optimal energy retrofit plan for a whole stock of buildings, optimizing efficiency, sustainability, and comfort, while effectively allocating the available financial resources to the buildings. The proposed methodology is applied to a real stock of public buildings in Bari, Italy. The obtained results demonstrate that the approach effectively supports the city governance in making decisions for the optimal management of the buildings’ energy efficiency.