<p>Natural stones have been used as basic building materials in many of the historical buildings and monuments that are cultural heritage from past to present. Limestones are the most preferred material group in many historical buildings and monuments in our country due to their aesthetic appearance and ease of workability. However, these stones are more easily affected by atmospheric conditions compared to other natural stones and gradually degrade over time due to physical, chemical, and mechanical effects. In order to make these Stones more resistant to degradation, there is a need to improve or reinforce their in-situ properties. Microbial consolidation is a new approach developed to recreate a structure similar to the original microstructure of a stone in order to achieve maximum compatibility in the consolidation of the stone. In this study, the effects of the microbial consolidation method on stones were investigated by using <i>Myxococcus xanthus</i> and <i>Bacillus subtilis</i> strains before and after the application of the mercury porosimetry test, mineralogical and petrographic analysis, color measurements, and scanning electron microscope (SEM) analysis. At the end of the study, total porosity values of Kufeki stone, Sazlıbosna stone, and Suloglu stone samples showed percentage decreases between 14–83%. Mineralogical, petrographic, and scanning electron microscopy (SEM) analyses revealed that calcium carbonate precipitation occurred in all stone samples. Bacterial cells completely covered the pore walls of the stones after the calcium carbonate precipitation. Bacterial cells are attached to the calcite grains without blocking the pores. The promising results obtained on the stone samples after the application of the microbial consolidation method showed that the use of bacteria offers potential as a new intervention method for the conservation of porous limestones sensitive to atmospheric conditions.</p>