Under natural conditions, peatlands store large amounts of soil organic carbon (SOC). However, they are under threat due to drainage which leads to mineralisation of soil organic matter to carbon dioxide (CO2). This situation is especially severe in Germany, where more than 70 % of peat and other organic soils are used for agriculture. This study assessed the properties of these soils within the framework of the first German Agricultural Soil Inventory. In a nationwide 8 × 8 km grid, soils from a total of 3104 sites were sampled to depths of up to one metre or down to the peat base. Of these sites, 146 were on peat and other organic soils; and 31 % of the 146 sites were being affected not only by drainage but also by changes in horizonation (e.g. mineral covers, deep ploughing). The classification of heavily disturbed sites is limited within the German Manual of Soil Mapping, which has led to the development of an adapted classification scheme for peat and other organic soils under agricultural use in Germany. The respective peat classes showed distinct patterns of SOC and total nitrogen (Nt) contents and stocks, bulk density (BD) and C:N ratios. Overall, a SOC stock of 529 ± 201 t ha-1 and a Nt stock of 29.3 ± 13.9 t ha-1 were found within a depth of 0–100 cm. However, in deeper profiles, 48 % of the total SOC was stored below 100 cm depth down to the peat base. High SOC stocks were also found in peat-derived, mineral-covered and deep-ploughed organic soils, which might be classified as mineral soils depending on the classification system used but are still prone to mineralisation and need to be considered in terms of emissions reporting and mitigation. Logarithmic and quadratic pedotransfer functions were developed to estimate BD and SOC density, respectively, from SOC contents. This is necessary for the calculation of SOC stocks when analyses of BD are absent. The quadratic relationship between SOC content and SOC density clearly showed that heavily degraded organic soils store as much SOC in a defined volume as more natural ones, and that any estimates of differences in potential CO2 emissions should not be based on SOC content, but on SOC density instead.