The present study examines the formation history and cryolithological properties of the late-Pleistocene Yedoma Ice Complex (IC) and its Holocene cover in the eastern Lena delta on Sobo-Sise Island. The sedimentary sequence was continuously sampled at 0.5 m resolution at a vertical Yedoma cliff starting from 24.2 m above river level (a.r.l.). The sequence differentiates into three cryostratigraphic units: Unit A, dated from ca. 52 to 28 cal kyr BP; Unit B, dated from ca. 28 to 15 cal kyr BP; Unit C, dated from ca. 7 to 0 cal kyr BP. Three chronologic gaps in the record are striking. The hiatus during the interstadial marine isotope stage (MIS) 3 (36–29 cal kyr BP) as well as during stadial MIS 2 (20–17 cal kyr BP) might be related to fluvial erosion and/or changed discharge patterns of the Lena river caused by repeated outburst floods from the glacial Lake Vitim in southern Siberia along the Lena river valley towards the Arctic Ocean. The hiatus during the MIS 2–1 transition (15–7 cal kyr BP) is a commonly observed feature in permafrost chronologies due to intense thermokarst activity of the deglacial period. The chronologic gaps of the Sobo-Sise Yedoma record are similarly found at two neighbouring Yedoma IC sites on Bykovsky Peninsula and Kurungnakh-Sise Island and are most likely of regional importance. The three cryostratigraphic units of the Sobo-Sise Yedoma exhibit distinct signatures in properties of their clastic, organic, and ice components. Higher permafrost aggradation rates of 1 m kyr−1 with higher organic-matter (OM) stocks (29 ± 15 kg C m−3, 2.2 ± 1.0 kg N m−3; Unit A) and mainly coarse silt are found for the interstadial MIS 3 if compared to the stadial MIS 2 with 0.7 m kyr−1 permafrost aggradation, lower OM stocks (14 ± 8 kg C m−3, 1.4 ± 0.4 kg N m−3; Unit B), and pronounced peaks in the coarse-silt and medium-sand fractions. Geochemical signatures of intra-sedimental ice reflect the differences in summer evaporation and moisture regime by higher ion content and less depleted ratios of stable δ18O and stable δD isotopes but lower deuterium excess (d) values during interstadial MIS 3 if compared to stadial MIS 2. The δ18O and δD composition of MIS 3 and MIS 2 ice wedges shows characteristic well-depleted values and low d values, while MIS 1 ice wedges have elevated mean d values between 11 ‰ and 15 ‰ and surprisingly low δ18O and δD values. Hence, the isotopic difference between late-Pleistocene and Holocene ice wedges is more pronounced in d than in δ values. The present study of the permafrost exposed at the Sobo-Sise Yedoma cliff provides a comprehensive cryostratigraphic inventory, insights into permafrost aggradation, and degradation over the last approximately 52 kyr as well as their climatic and morphodynamic controls on the regional scale of the central Laptev Sea coastal region in NE Siberia.