The coatings of microorganism-induced calcium carbonate onto the stone surface carried out by using both of the immersion method and coating method were investigated. Various analysis and testing techniques such as scanning electron micrograph (SEM) and X-ray diffraction (XRD) were used to characterize the deposited mineral layer. The adhesive property, acid resistance, frost resistance, light and aging resistance, water adsorption and permeability were investigated in detail. The results showed that both immersion method and coating method could produce calcium carbonate granules with sizes ranging from 1 to 10 μm and form a layer of dense mineralization membrane which is about 50 to 100 μm thick. Immersion method was more efficient than coating method. The large cohesive force between calcium carbonate layer and stone materials could improve the acid rain resistance as well as excellent heat tolerance, frost resistance and light aging resistance. The coating process could not only help the stone materials maintain its original permeability with the aid of calcium carbonate layers but also improve the penetration resistance significantly. Therefore, this type of technology shows a great potential in the protection of stone relics.