Numerical models play a primary role in Cultural Heritage preservation. Nevertheless, the design of a realistic model remains challenging due not only to the complex behavior of masonry but also to the asynchronous building phases, the damage induced by natural and anthropic aggression, and the associated repairs. This paper discusses the impact of the information provided by an in-depth analysis of the construction history on the updating process of a Finite Element building model. The case study is the church of Sant'Agata del Mugello (Italy); for this building, a previous historical-archaeological study identified and recorded the asynchronous construction phases, the repair techniques, and the damage induced by three historical earthquakes (1542, 1611, and 1919)—moreover, a dense ambient vibration survey allowed to identify the modal parameters. The information from previous works is summarized in five Finite Element models with increasing complexity. A vibration-based model updating methodology based on a Particle Swarm Algorithm is developed. This work shows that the best minimization of the difference between the numerical and experimental modal parameters is obtained with the numerical model considering the identified construction techniques, repair phases, and connection relations between the bell tower and the nave.