A comparative study of the influence of microorganisms on physical-chemical clays’ properties at different lithogenetic stages concerned the formation of contact strength between particles was carried out. Natural samples were taken for experiments: dolomite-clay marl from outcrop, the Jahorina mountains, the Dinaric Alps, Bosnia and Herzegovina; alluvial loam from spring, West side of the Onega Lake, Konchezero village, Karelia Republic, Russia; bentonite from the Biklyan deposit, Tatarstan Republic, Russia; phyllite from outcrop, Les Sybelles, Rhone Alps, France. The microbial community was added into moistened clays for 2-4 months. Before and after the experiments such analyses were conducted: X-ray powder diffractometry, determination of water content in clays, maximum hygroscopicity, dry bulk density, total organic carbon, macroscopic wetting contact angle, liquid and plastic limits; incremental loading oedometer test, ion chromatography of filtrate. The microbial activity enhanced the hydrophilicity of marl and phyllite. Multidirectional factors of toughness formation acted in clays subjected to stages between sedimentogenesis and late diagenesis, among which organic matter content dominated.