Granite rapakivi was widely used in the construction of historical buildings in St. Petersburg. This rock was mined in Karelia and southern part of Finland where old quarries are preserved. Biofouling of granite can be observed both in urban environments and in natural outcrops. Biofilms on granite rapakivi have a different structure, composition, speed of development. The aim of this work is the complex analysis of biological colonization of granite rapakivi in different environment. The biodiversity of biofilms was studied on granite monuments of Saint Petersburg as well as in the abandoned quarries of the southern part of Finland. The composition of micromycetes, cyanobacteria and organotrophic bacteria in biofilms was determined at different stages of colonization and destruction of the granite rapakivi. The composition of metabolites in biofilms and sediments on the surface of the rock was determined. More than 200 compounds were found in the samples from the quarry and about 60–100 low molecular weight organic compounds were detected in the samples from the urban environment. Concentration of certain compounds, especially polyols, was significantly higher in biofilms in the urban environment. The main features of biological colonization of granite rapakivi in the urban environment and natural outcrops were shown by scanning electron microscopy. The differences in the character of colonization of feldspar, quartz and mica were revealed. It was found that under the influence of bacteria Bacillus subtilis the intensity of elements leaching from granite minerals in the aquatic environment (model experiment) was significantly increased. Feldspars and mica were destroyed first of all.