Rock erosion is attracting increasing attention from scientists worldwide. The area encompassing the Saint John Baptist Church, Saint John Village, XVII century ruins in Rio Grande do Sul at the UNESCO World Heritage Site is considered a Brazilian treasure. However, the risk of damage to this site from rock erosion has recently increased tremendously. Generally, the rocky construction such as fence, wall and tomb stone, seems strong but is actually extremely sensitive to erosion caused by lichens, fungi, molds and bacteria. Because of biological erosion and massive exposure, the fresh rock is dominated by clays and microorganisms. Water-adsorbing clays and microorganisms influence the mechanisms of the rock erosion. In this study, the formation of bio-clay-minerals in porous structure of pisolite was demonstrated using electron microscopy. Bacterial clay mineralization can deform the rock structure and even produce organic materials. Biological activity could easily corrode rocky constructions around the Saint John Baptist Church site. The rocks are pisolitic laterites possibly formed in Tertiary over the Kretaceous Parana flood Basalts. Samples inhabited by lichens and fungi were collected from a collapsed wall in the ancient church. The zonal reddish-brown pisolites are 4 mm in diameter in a matrix of clays associated with porous and empty spaces. Elemental distribution maps from X-ray fluorescence microscopy show iron-rich spherules of pisolite, whereas the matrix is composed of Al, Si, Mn, and Sr; thus producing goethite and kaolinite. Transmission electron microscopic observation showed that various types of bacteria inhabit the spherule and are associated with clay minerals and graphite. STEM elemental analysis confirmed the bio-clay-mineralization with Al, Si, S, and Fe, around bacterial cells. The results presented here will improve our understanding of nm-scale bio-mineralization and bio-erosion in lateritic rocks.