Several lime mortars for the repair of painted plasters of the rock-cut church of Ss. Pietro and Paolo in Matera were studied. They were designed taking into account both aesthetic criteria that need to be fulfilled in the field of paintings restoration, and physical-mechanical compatibility with the original materials on site, i.e., the pre-existing plasters and the supporting rock. Mixes with calcareous and silica aggregates, based on different grain size proportions, were prepared to fill missing portions of the original painted plaster. The effects of the mineralogical nature and size of the aggregates on the characteristics and properties of the mixes were investigated in relation to the microstructure, physical-mechanical features and resistance to salt ageing. At the end of the experimental campaign, the overall performance was evaluated.