Calcareous stones have been largely used to build historical buildings. Among these, the calcarenites are usually characterized by a high content of calcite and a high open porosity, which make them very sensitive to the weathering caused by physical and chemical agents. In order to prevent their deterioration and to retard their decay, different protective products-mainly polymers-are applied on the stone artefact surfaces. In this work we apply the methodology tested in a preliminary study to investigate the morphological changes of the internal structure of a biocalcarenite (Lecce stone) by micro x-ray computed tomography (micro-CT). The porosity and other morphological parameters of the rock before and after the conservation treatment were calculated on a significant number of samples. The Student's t test was applied for statistical comparison. The results reveal that the treatment with Paraloid B72 (PB 72) is homogenously distributed and causes small changes to the natural properties of the rock, whereas the application of a fluoroelastomer (NH) causes an appreciable decrease in porosity and variation in terms of wall thickness distribution, probably resulting from its inhomogeneous distribution.