Vibration-based structural monitoring methods have been widely used in recent years for the evaluation of the dynamic performance and damage assessment of a wide scenario of civil structures. They represent powerful tools in the civil engineering field because they are able to provide real-time information on the structural health state during the structural life or after a catastrophic event (e.g. earthquake, hurricane). For this aim, it is evident that the numerical procedure used to obtain the possible damage state must be reliable and efficient in time-demand. Finite Element (FE) model updating techniques based on ambient or forced vibrations are tools able to localize a damage identified as a change in the structural stiffness starting from the vibration response measurements. The assessment of uncertainty of the identified parameters is of significant relevance especially for damaged structures and when the decision-maker has to decide to close a bridge or a building to prevent any effect of a possible collapse of the structure. This paper describes the results of the modal updating of an historical masonry fortress damaged by the seismic event that hit the town of San Felice sul Panaro and the surrounding localities in the Po Valley in the 2012. A standard updating procedure and a Bayesian procedure are first applied to calibrate the complex FE model of the fortress with respect to experimental modal data. The uncertainty of the identified parameters of structural systems is then evaluated by using the Bayesian probabilistic approach. The most probable parameter vector is obtained by maximizing the posterior probability density function. The robustness and the efficiency of the procedure are assessed through the comparison with the results obtained from the estimation of the Pareto-optimal solutions.