Heritage buildings often results from prolonged construction processes that leave discontinuities and joints in masonry walls. These features compromise the overall box-like behavior and trigger local failure mechanisms, making preliminary experimental and numerical studies on their dynamic behaviour essential. Villa Gazzotti in Bertesina (Vicenza) offers a representative case, combining multiple construction phases and the integration of a preexisting structure. Archaeological analysis of the façades clarified the extent of each phase, which was not evident from historical documents. Despite the presence of discontinuities, dynamic identification tests revealed a predominantly overall structural response, with the two parts of the building vibrating in phase. Finite element analyses confirmed a limited sensitivity to the modeling of discontinuities as interfaces. The behavior is likely influenced by the continuity provided by timber floor slabs and iron ties introduced during construction. Calibration of the numerical model required reducing the elastic modulus, due to widespread cracking, and increasing material density—possibly indicating internal infill of thick masonry walls. Further tests are planned to confirm these assumptions.