The cultural significance of historical buildings uniquely represents the heritage of nations. Previous destruction of historical buildings offers valuable data for researchers to document the behavior of such buildings. Non-destructive techniques, such as Finite Element Modeling (FEM), are used to investigate the complex response of historical buildings considering the linear and nonlinear Responses. In this paper, the numerical investigation of two historical buildings in Cyprus are investigated using FEM. These buildings are situated in the historical city of Famagusta Walled City, where many huge Cathedrals to small chapels are available. Two nearby masonry historical buildings (Ruins of Saint Mary of Carmel and Church of St. Anne) are investigated. Both buildings share the same style, subgrade, and orientation. However, one of the buildings was subjected to roof damage under certain previous earthquakes, while the second one remained safe. Time history analysis was conducted using historical earthquake data beside the effect of gravity loading and considering three-dimensional elements of buildings. Properties of stone and mortar are tested experimentally while adaptive mesh size is selected. In this research, stresses and relative displacements between key nodes are investigated to document the main reasons for the collapse. Results showed that the size of stone and elemental ratios of architectural forms had a valuable impact on changing stresses and exceeding relative displacement in one of the buildings causing the observed damage. Excessive displacement was one of the evidence of roof failure as the material cannot sustain high deformation.