Recent Italian earthquakes have shown the seismic vulnerability of many typical historical masonry churches characterized by one nave and wooden roofs. Under transverse earthquake the nave transverse response of this kind of churches can be influenced by the geometrical and material features. To increase the seismic performance, strengthening interventions aimed to pursue the global box-behavior by the realization of dissipative roof-structure represent a valid strategy especially for avoiding out-of-plane mechanisms. In this way, the roof structure must be able to represent a tool for the damped rocking of the perimeter walls. Cross-laminated timber panels (CLT) have been recently adopted as roof-diaphragm having shown valid ductile behavior in experimental tests, satisfying the conservative restoration criteria at the same time. In this paper, after a description of the numerical approach for the damped rocking mechanism for one nave configuration church, the effectiveness of different CLT based roof-diaphragms in the nave transverse response is investigated for four historical churches. The seismic responses are performed by comparative dynamic nonlinear analyses and the results are shown in terms of displacements and shear actions transferred to the façade. The influence of the geometrical features of the churches on the nave transversal response is deepened by sensitivity analyses with the aim to predict the displacements and shear variations under the same earthquake excitation.