Toxic substances are often employed in conventional stone preservation techniques, whereas biorestoration offers material compatibility along with significant benefits for cultural heritage preservation, environmental safety, and sustainability. However, the application of this innovative technique to natural rocks is not fully understood. In this study, we evaluated the efficiency of a carbonatogenic bacterial strain (Lysinbacillus fusiformis 3.20) on three natural carbonate rocks: Calcarenite (CA), Travertine (TR) and Marble (MA), having different porosities. We integrated surface analyses (Field Emission Scanning Electron Microscopy, Atomic Force Microscopy, and X-Ray Diffraction) with bulk analyses (Porosity, Ultrasonic Wave Velocity, and Dynamic Elastic Moduli) to investigate the bioconsolidation processes. The results indicated that the biomineralization treatment had no effect on MA samples, while it improved the physical and mechanical properties of both CA and TR, evidenced by the formation of new bioprecipitates. Total and effective porosity decreased, particularly in CA, while ultrasonic wave velocities (Vp and Vs) and Young's modulus increased, with Poisson's ratio remaining unchanged. Comparative observations suggest that connected, randomly distributed, and low aspect ratio pores facilitate microbial activity by enabling deeper bacterial penetration into the stone, supporting nutrient distribution and the formation of calcium carbonate precipitates. When the treatment is effective, stiffness and strength are expected to increase due to reduced effective porosity, while resistance to shear deformation remains nearly constant, as does the relationship between porosity and wave velocities.