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The present research paper properly focuses on the dynamics and failure mechanisms of the masonry “Apennine Church” of Santissimo Crocifisso in Pretare, municipality of Arquata del Tronto in the province of Ascoli Piceno (Marche region, Central Italy). Such a peculiar structural type traditionally characterizes the intense seismic area of Central Italy, unfortunately almost totally damaged by the recent shock sequence of 2016. Advanced numerical modeling through discontinuous and continuous approaches were here utilized to have an insight into the dynamic properties and behavior of the structure under strong nonlinear dynamic excitations. In the discrete element approach, the non-smooth contact dynamics method, implemented in LMGC90©, was applied, adopting a full 3D detailed discretization. The church was schematized as an arrangement of rigid blocks, subjected to sliding by friction and perfect plastic collisions, with a null restitution coefficient. In the finite element approach, the concrete damaged plasticity model available in Midas FEA NX© was involved. This model allows reproducing the tensile cracking, the compressive crushing, and the degradation of the material under cyclic loads. Finally, the numerical analyses provided a valuable picture of the actual behavior of the church, thus giving useful hints for future strengthening interventions.