Many typical historical masonry churches, with one nave and wooden roofs, have shown high seismic vulnerability in the recent seismic events, especially under transverse earthquakes. In fact, the nave transverse response of this kind of constructions is influenced both by the materials features and the geometrical characteristics. In order to improve the seismic response, the box behavior strategy basing on dissipative roof-diaphragm, can be pursued by adopting cross laminated timber panels (CLT). In this paper, for five historical masonry churches, the effectiveness of different CLT panels solutions is investigated by performing comparative nonlinear dynamic analyses adopting equivalent finite element models. The CLT solutions differ themselves for the panels thickness (6mm and 10mm) and the number of the connections (8,16 and 32 crews in one linear meter). The results are shown in terms of dimensionless transverse displacement (drift) and shear occurred at the base of the façade. Therefore, the influence of the most important geometrical features (as slenderness of the perimeter walls, the width and the length of the churches) in the seismic response is pointed out for each church equipped by different CLT roof-diaphragm solutions.