Cultural and religious heritage assessments and restorations are considered to be a fundamental requirement of any modern society because these constructions represent one of the most meaningful and tangible connections to our past. With rare exceptions, heritage buildings were built with materials and systems that could bear gravitational loads but not bending and shearing resulting from seismic loading. Thus, in many cases, earthquake ground motions have led to severe degradation and even the collapse of various parts of these structural systems. In order to address these issues, repair and replacement techniques are applied as common parts of restoration work. In the peculiar case of stone masonry structures, a standalone macroscopic examination is not self-assured and, most often, can lead to an inadequate selection of a replacement material. Therefore, a knowledge of mesoscopic, petrographic, physical and mechanical properties is compulsory in the design, planning and execution of restoration work. From this perspective, the present research has taken, as a case of study, the Frumoasa monastic complex from Iași, Romania, introducing microscopic, XRF (X-ray fluorescence) spectroscopy and petrographically based approaches, comparing three limestone samples with a sample dislodged from the original wall. The physical properties (bulk and real densities, open porosity and capillary water absorption coefficient) and the mechanical properties (compressive and tensile strengths) were also experimentally determined. The samples were extracted from stone quarries located on the territories that were part of the same historical region as the Frumoasa monastic complex. Based on the outcomes of this study, suitable criteria for the stone replacement—consisting of identifying the main structure, quarry rock petrographical parameters and physical and mechanical characteristics—were determined and applied.