Italian military heritage is a highly consistent and heterogeneous building stock, often unknown, and distinguished by a significant historical-artistic value. The urge for maintenance, restoration, and re-functionalization works on this diffuse real estate has to face some crucial and often contrasting issues. The need to improve the energy efficiency of military existing buildings must deal with their values and peculiarities. Pursuing both the active protection of the building heritage and the improvement of its energy performance generates unavoidable conflicts. This contribution presents a multi-disciplinary methodology aimed at planning and evaluating intervention scenarios on the military building stock, balancing all the aspects involved. This methodology connects different technologies for detailed geometric surveys, the raumbuch and the Heritage Building Information Model as effective tools for knowledge analysis, classification, and integration. The findings of experimental applications of the proposed methodological approach to the Alberto Riva Villasanta barrack in Cagliari, a twentieth century architectural military complex, are finally presented and discussed.