The paleopedology of the world’s largest retrogressive thaw slump, Batagay, is understudied. Micromorphological and geochemical analysis reveal the properties of th host sediments and major pedogenic features. Epigenetic soil profiles of Marine Oxygen Isotope Stage (MIS) 7 (or older) and 5e are clearly distinguished and well developed due to favorable bioclimatic conditions for pedogenesis, probably similar to modern ones. The oldest unit contains a paleosol similar to a Histic Reductaquic Cryosol, indicating a peat-covered, boggy environment. The MIS 5e unit contains organic-rich Histic Spodic Cryosol with well-developed structure, formed during the interglacial optimum, which was relatively warm and presumably resembled modern bioclimatic conditions. MIS 4–3 deposits contains soil-like bodies enriched in coarse organogenic material resembling incipient Histic Reductaquic Cryosols. Interglacial/interstadial units contain micromorphological evidence of aggregate and pore formation, Fe-oxide and organic matter redistribution and clay accumulation. Stadial deposits show weakly expressed soil structure with uneven aggregates, cryogenic disintegration of plant detritus and rare evidence of accumulation of humic substances. Major elemental ratios indicate intensification of biochemical weathering in paleosols and soil-like bodies. Pedogenically reworked material of stadial sedimentary units with sporadic and incipient soil-like bodies provide a significant source for paleoenvironmental reconstruction of harsh Late Pleistocene environments.