The research concerns the case-study of the church of Santa Maria del Popolo into the historical Incurabili Hospital in Naples, seriously damaged during a bombing raid in 1943. The construction of a reinforced concrete trussed roof and floor above the main nave has caused serious structural problems and the church shows evident signs of deterioration today. The present situation offers the occasion to deep, in an interdisciplinary way, the delicate issue of the recent past strengthening operations realized with reinforced concrete that, associated with highly territorial seismicity, alarm about the condition of many historical buildings. In order to have a clear knowledge of the structural behavior of the church, assessing the actual in situ condition, a numerical FE analysis has been performed with the scope of evaluating the state of stress in the structural elements of the walls and of the roof, pointing out the structural deficiencies. The numerical damage assessment has been validated by means of comparisons with crack patterns. Providing a reliable model, it has been possible to fully simulate the behavior of historical structures when subjected to different and severe types of load, e.g. seismic loads.