Observations of post-earthquake damage highlight the remarkable seismic vulnerability of historic masonry bell towers. This is due to the combination of geometric slenderness, poor quality of masonry, and inadequate connections between walls. The seismic assessment of these structures represents a pivotal issue in the field of cultural heritage conservation. A great research effort has been made to predict the seismic behaviour of bell towers through finite element modelling. The reliability of results depends on the accuracy of the geometric model, which can rely on the high precision of the digital survey, and on the proper calibration of the mechanical properties of the material, which can be performed through dynamic-monitoring based model updating. Within this framework, the present work investigates the dynamic behaviour of the bell tower of Madonna della Quercia Sanctuary, in Viterbo (Italy), through a model updating process performed in a distinct element method (DEM) environment. First, a digital survey was carried out on both the exterior and the interior of the tower and a 3D geometric blocky model was generated and imported into 3DEC DEM code. In this operation, orthophotos were used to derive the blocks arrangement of the outer wall leaves, whereas the core was filled in through parametric modelling. Then, environmental vibrations were recorded using triaxial velocimeters and the main natural frequencies and mode shapes of the tower were obtained through operational modal analysis (OMA). Based on OMA results, the 3D DEM model was updated, by calibrating the normal and tangential joint stiffness. Experimental (OMA) and numerical (DEM) outcomes are compared in the paper, by highlighting strong points and limitations.