This article describes a methodology for the non-linear analysis of existing masonry structures subjected to external yielding constraints, with particular attention to the historical and cultural heritage constructions. It is well known, indeed, that most of the arch and wall damages are often due to settlement of abutments, in the former case, and to settlement of foundations, in the latter one. The ability to observe and correctly analyze the cracking failure pattern, visible on such structures, is the main “diagnostic tool” for identifying its origin: the modification of load conditions over time, foundation settlements and earthquakes. The objective of this work is to identify a numeric modelling of masonry structures (such as walls, arches, vaults, ruins) under any load condition and subjected to inelastic settlements impressed to some external constraints. The purpose of the numerical procedure is to interpret the behaviour of such structures in order to assess both the peak settlement value and their specific failure mode in correspondence to a geometry which is very often compromised. Therefore, this procedure allows one to estimate the degree of the structures’ vulnerability, in order to prevent any future damage, both local and global. The iterative algorithm proposed in this article, developed in a calculation software, processes the structure considering, not only the properties of constitutive material, non-homogeneous and anisotropic, but also the change of the structure’s shape during the settlements increase. In this way a non-linear analysis is performed both materically and geometrically. Through a direct comparison between numerical and experimental results, obtained by testing some simple structural models in a laboratory, it was ascertained, both from a qualitative and quantitative point of view, the correctness and the efficacy of the proposed procedure, which will be explained below. Therefore, this numerical procedure demonstrates to be a useful “diagnostic tool” by which, starting from the input of the masonry structure to be studied and simulating a presumable event, one can trace the source of the causes that have generated a certain failure, comparing the cracking pattern of real structure with that plotted by the software.