Permafrost deposits constitute a large organic carbon pool highly vulnerable to degradation and potential carbon release due to global warming. Permafrost sections along coastal and river bank exposures in NE Siberia were studied for organic matter (OM) characteristics and ice content. OM stored in Quaternary permafrost grew, accumulated, froze, partly decomposed, and refroze under different periglacial environments, reflected in specific biogeochemical and cryolithological features. OM in permafrost is represented by twigs, leaves, peat, grass roots, and plant detritus. The vertical distribution of total organic carbon (TOC) in exposures varies from 0.1 wt % of the dry sediment in fluvial deposits to 45 wt % in Holocene peats. Variations in OM parameters are related to changes in vegetation, bioproductivity, pedogenic processes, decomposition, and sedimentation rates during past climate variations. High TOC, high C/N, and low δ13C reflect less decomposed OM accumulated under wet, anaerobic soil conditions characteristic of interglacial and interstadial periods. Glacial and stadial periods are characterized by less variable, low TOC, low C/N, and high δ13C values indicating stable environments with reduced bioproductivity and stronger OM decomposition under dryer, aerobic soil conditions. Based on TOC data and updated information on bulk densities, we estimate average organic carbon inventories for ten different stratigraphic units in northeast Siberia, ranging from 7.2 kg C m−3 for Early Weichselian fluvial deposits, to 33.2 kg C m−3 for Middle Weichselian Ice Complex deposits, to 74.7 kg C m−3 for Holocene peaty deposits. The resulting landscape average is likely about 25% lower than previously published permafrost carbon inventories.