Nearly-zero energy buildings are now a standard for new constructions. However, the real challenge for a decarbonized society relies in the renovation of the existing building stock, selecting energy efficiency measures considering not only the energy performance but also the economic and sustainability ones. Even if the literature is full of examples coupling building energy simulation with multi-objective optimization for the identification of the best measures, the adoption of such approaches is still limited for district and urban scale simulation, often because of lack of complete data inputs and high computational requirements. In this research, a new methodology is proposed, combining the detailed geometric characterization of urban simulation tools with the simplification provided by “building archetype” modeling, in order to ensure the development of robust models for the multi-objective optimization of retrofit interventions at district scale. Using CitySim as an urban scale energy modeling tool, a residential district built in the 1990s in Bolzano, Italy, was studied. Different sets of renovation measures for the building envelope and three objectives —i.e., energy, economic and sustainability performances, were compared. Despite energy savings from 29 to 46%, energy efficiency measures applied just to the building envelope were found insufficient to meet the carbon neutrality goals without interventions to the system, in particular considering mechanical ventilation with heat recovery. Furthermore, public subsidization has been revealed to be necessary, since none of the proposed measures is able to pay back the initial investment for this case study.