Preserving Italy’s rich historical and artistic heritage is a top priority for both Italian and International policymakers. This heritage comprises a diverse array of masonry buildings constructed using various materials and techniques, resulting in different potential damage scenarios that may necessitate suitable retrofitting measures. To conduct a precise structural analysis, particularly under horizontal loading conditions, it is essential to formulate a sound seismic assessment. While numerous numerical tools are available for this purpose, each approach begins with certain assumptions that cannot be universally applied. This study aims to compare two distinct modelling techniques, assessing their respective strengths and weaknesses. To achieve this objective, we selected an earthquake-damaged complex in central Italy as a case study. The structure was modelled using both a Finite Element (continuous) method and a Distinct Element (discontinuous) method. Subsequently, both approaches underwent nonlinear dynamic analyses utilizing recorded strong motion data from the 2016 seismic events. The findings indicate that both methods can effectively identify structural weaknesses. However, in certain instances, the Distinct Element method exhibited greater accuracy in replicating the presence of cracks.