Identifying the possible causes of existing damage in historical structures is a complex task. Common difficulties are the limited information regarding the history of the construction, the properties of materials and the morphology of structural members. This paper investigates the capability of advanced numerical modelling to address the aforementioned issues and to simulate the damage in complex masonry structures. The case under study is the church of the Poblet Monastery, one of the UNESCO World Heritage Sites in Spain. The developed finite element model includes the actual-deformed 3D geometry of a selected bay, aiming to consider the important deformation of the structure during the analysis. Based on the historical survey, the analysis considers different hypotheses to investigate on the possible causes of existing damage: gravitational loading, settlements , past earthquakes and reported structural alterations. The influence of the material parameters on the structural safety is assessed with parametric analysis. Additionally, the parallel use of graphic statics with numerical analysis helps to interpret realistically the structure’s current equilibrium. The applied numerical strategy is effective to understand the causes of the present damage in the structure. The results of the study are useful to make a first diagnosis and are the prelude for future inspection, testing and monitoring activities ; Peer Reviewed ; Postprint (published version)