The formation of biolayers of various taxonomic and biochemical composition occurs on the rock surfaces under various environmental conditions. The composition of metabolites in various types of biolayers on the marble surface in natural outcrops and urban environment was stud-ied. Metabolome profiling was fulfilled by GC‐MS. It was found that communities in urban environment are much less biochemically diverse than in a quarry. The seasonal differences in metabolite network between samples dominate over taxonomic ones in biolayers with predomination of algae and cyanobacteria and in biolayers with predomination of fungi. The biolayers of different stage of soil formation are less susceptible to seasonal variability.