Differential soil settlements can induce structural damage to heritage buildings, causing not only economic but also cultural value losses. In 1963, the Saint Jacob’s church in Leuven was permanently closed to the public because of severe settlement-induced damage caused by insufficient bearing capacity of the foundation. Currently, the church is stabilized using a temporary shoring system. This work aims at implementing a practical modelling approach to predict damage on church nave walls subjected to differential settlements. For that purpose, a finite element model of the Saint Jacob’s church nave was generated and validated through on-site monitoring data including levelling, damage survey and laser scanning. The model takes into account the non-linear behavior of the masonry by means of continuum smeared cracking. The paper introduces two approaches to model the settlement on the structure. One of them consists in the direct application of vertical displacements underneath the structure according to the deformation profile measured on-site. In the second approach, interfaces with different stiffness are placed at the base allowing the structure to deform under its self-weight. In addition, the effect of the settlement profile type in the damage level is analyzed.