Historic buildings are complex structures in which all the composing elements work together. Studies of heritage structures after seismic events have shown that timber roof structures strongly influence the seismic response of masonry structures, being able to reduce or enhance the out-of-plane displacement of the structure. Starting from these observations, three different types of roof structures, from the eighteenth, nineteenth and twentieth centuries, were introduced in the finite-element simulation software SCIA Engineer. The roof structures were subsequently placed on the same eighteenth-century masonry building with a ground floor and two upper floors, respecting its geometric features. Simulations were performed considering successively rigid, hinged or sliding connections between the roof and the masonry structure. At the same time, the traditionally crafted joints of the roof structures were consecutively modelled as hinged, rigid and semi-rigid (determined using three different methods). Ultimately, the top horizontal displacement, inter-storey drift and damage level of the masonry structure were compared. The main aims of this study were to observe if roof structures have an influence on the seismic behaviour of masonry buildings and to determine if selected parameters suffer any changes depending on the roof structure type, the roof–wall connections and joints’ axial stiffness.