The architectural heritage is subjected to various risk factors like the lack of maintenance, the material decay and the external solicitations. Nowadays, due to the ever-increasing demand for urban space, a relevant cause of structural damage that the historical buildings experience is the ground settlement due to excavation works. In the city of Amsterdam, for example, the construction of the new North-South metro line will involve an area characterized by the presence of many ancient masonry buildings. A fundamental phase of the design of this kind of projects is the assessment of the risk of subsidence which can affect the existing structures. The actual method to perform this assessment provides for a preliminary screening of the buildings located in the area surrounding the excavation, in order to evaluate which structures are at risk of settlement induced damage. It is based on the simplification of the building as a linear elastic beam and the assumption of the absence of interaction between the soil and the structure. An improved classification system should take into account the main parameters which influence the structural response, like the nonlinear behaviour of the building and the role played by the foundation in the soil-structure interaction. In this paper, the effect on the damage mechanism of the excavation advance and the location of the tunnel with respect to the building is evaluated. Numerical analyses are performed in order to understand the effect of different settlement profiles of the ground. A coupled model of the structure and the soil is evaluated, taking into account a damage model for the masonry building and the nonlinear behaviour of the soil-structure interaction. This paper demonstrates the importance of 3D modelling; neglecting the tunnel advance can lead to an underestimation of the damage.