From the theoretical point of view, systems composed by masonry arches or vaults would require, during construction, the simultaneous activation of all structural elements in order to reach the optimum balance of thrusts. This is not obviously the case of complex ancient masonry constructions, whose long and gradual building process may have contributed to their deformed condition and even to damage. In this paper, the possible influence of the construction process as well as that of later long-term deformation on the final condition of the building is investigated in the case of a complex and large historical structure, namely Mallorca Cathedral. A FE code has been specifically developed for the present study. The code is able to account for construction processes through sequential-evolutionary analyses, with the description of masonry mechanical damage and long-term deformation. The representative bay of the cathedral is analyzed taking into account different construction phases, as emerged from historical research. The response of such substructure to transverse earthquake equivalent forces is then investigated. In this case, the damage model is improved with a local crack-tracking algorithm. This numerical strategy models the tensile damage as distinct cracks, leading to a better prediction of realistic collapsing mechanisms. ; Postprint (published version)