The influence of the natural hydraulic lime-based grout on the dynamic behaviour of injected multi-leaf stone masonry elements is discussed in the paper. Shaking table experiments on two stone masonry buildings, tested before and after grout injection, have been performed. The paper focuses on the analysis of both the recorded accelerations and related displacements, at the bottom and at each further storey. This leads to evaluate the stiffness of the unstrengthened and injected structures. The input at increasing PGA allowed the stiffness decay to be studied, simulating a gradual damaging of the structures. These results were also interpreted in the light of both computed frequencies and mode shapes. Finally, the comparison among these results, obtained from all the models, allows to deepen the knowledge concerning the effects induced by the lime-based grout injection and on its capability to modify the dynamic behaviour, when intervening on a damaged (repairing) or on an undamaged (strengthening) structure.