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This paper investigates the dynamic characteristics and Finite element model updating of two confined masonry buildings in Messina, constructed in the aftermath of the devastating 1908 earthquake. The study addresses the need for advanced research in this field to enhance the understanding of the dynamic behaviour of confined masonry structures. The authors identified the modal parameters of the buildings from ambient vibration tests. Finite element models have been developed and fine-tuned in a second step to optimize the agreement between the simulated and observed modal parameters. The optimized parameters are then compared with the outcomes of nondestructive tests on masonry and reinforced concrete. This research addresses the modelling issues when dealing with confined masonry structures, offering guidance to engineers to select the modelling parameters. The paper emphasizes the substantial stiffening effect introduced by confined masonry, as evidenced by the optimized Young's modulus of masonry, which is almost two and a half times higher than values obtained from flat jack tests. To accurately represent the interaction between reinforced concrete ties and masonry panels within equivalent frame models, it becomes crucial to adequately overstate the masonry stiffness to capture the mutual coupling between structural components. • Dynamic characterization of confined masonry buildings. • Intelligent Automated Operational Modal Analysis approach. • Predictive capabilities of simplified FE modelling for confined masonry. • Genetic optimization algorithm to fine-tune modelling parameters. • Insight to select model parameters for confined masonry. [ABSTRACT FROM AUTHOR]