Due to their architectural and historical value, heritage buildings are among the most extensively studied structures, with particular attention to their seismic vulnerability. In this paper, two case studies located in the seismic active zone of Gerace (Reggio Calabria, Italy) have been deliberately selected. The chosen case studies are two peculiar churches built with irregular limestone blocks and mortar. A recently proposed Iterative Finite Element Upper Bound limit analysis approach is applied to investigate the behavior of the masonry churches under lateral loads. The procedure requires discretizing the structures into hexahedral rigid elements and simulating their interaction using interfaces. The interfaces exhibit rigid plastic behavior, enabling sliding and rotation between them, and mimic the realistic behavior of a masonry compound. The two case studies are analyzed following an iterative procedure to obtain convergence of the results and avoid parasite failure mechanisms imposed by stalling between elements or enforcing a no-tension material. The most prone active mechanisms are investigated for both churches. The collapse multiplier is automatically calculated, and the corresponding peak ground acceleration is obtained for each identified failure mechanism. Additionally, the study investigates the effectiveness of a retrofitting strategy in enhancing the seismic performance of the two churches.