The paper investigates the dynamic characterisation, the numerical model tuning and the seismic risk assessment of two monumental masonry towers located in Italy: the Capua Cathedral bell tower and the Aversa Cathedral bell tower. Full-scale ambient vibration tests under environmental loads are performed. The modal identification is carried out using techniques of modal extraction in the frequency domain. The refined 3D finite element model (FEM) is calibrated using the in situ investigation survey. The FEM tuning is carried out by varying the mechanical parameters and accounting for the restraint offered by the neighbouring buildings and the role of soil–structure interaction. The assessment of the seismic performance of the bell towers is carried out through a nonlinear static procedure based on the multi-modal pushover analysis and the capacity spectrum method. Through the discussion of the case studies, the paper shows that the modal identification is a reliable technique that can be used in situ for assessing the dynamic behaviour of monumental buildings. By utilising the tuned FEM of the towers, the theoretical fundamental frequencies are determined, which coincide with the previously determined experimental frequencies. The results from seismic performance assessment through a pushover analysis confirm that the masonry towers in this study are particularly vulnerable to strong damage even when subjected to seismic events of moderate intensity.