An extensive experimental campaign has been conducted at EUCENTRE in order to understand the dynamic behaviour of historic stone masonry structures and to evaluate the seismic performance of selected strengthening strategies, aiming at improving wall-to-floor connections and in-plane diaphragm stiffness. Shaking table tests were performed of three full-scale two-storey buildings made of undressed double-leaf stone masonry and timber floor and roof. Because of the asymmetric configuration of the buildings, different types of response were observed in the specimens for increasing levels of seismic input. The first prototype exhibited in-plane distortion of the flexible diaphragms and local out-of-plane failure modes were activated. In this paper the characteristics of the strengthening interventions on the second building prototype are described, where the connections between the floor and roof diaphragms and the walls were improved and only a moderate stiffening of the wooden diaphragms was made. The results obtained during the dynamic tests will be illustrated, focusing on the response of the structure, the damage mechanism and its evolution during the tests. The improvement of the connections proved to be very effective, increasing significantly the seismic capacity of the building with respect to the first prototype.