The DOK trial in Therwil (CH), compares bioorganic (BIOORG), biodynamic (BIODYN) and integrated (CONFYM) farming systems at two farmyard manure intensities corresponding to 0.7 and 1.4 livestock units per hectare with a purely mineral fertilized system (CONMIN) and an unfertilized control (NOFERT) since 1978. The treatments differ in plant protection and receive farming system specific organic matter inputs differing in rate and quality. SOC contents increased in BIODYN 1.4, less in BIOORG 1.4, and were stable in CONFYM 1.4. Enhanced biological soil quality under organic and particularly biodynamic management highlights the immanent relation between soil biology and SOC changes. Systems fertilized with manure of 0.7 livestock units and CONMIN lost SOC, but loss was highest in NOFERT. The impact on soil quality was only detectable after 20 years of continuous management. We conclude that recycling of the manure from 1.4 livestock units per hectare allows to maintain SOC levels and that the investment in producing manure compost from the same number of livestock is needed to enhance SOC levels and improve biological soil quality. The data come from 96 field plots (8 farming systems, 3 subplots with crops from a temporally shifted 7-year crop rotation, 4 replicates). Soil organic carbon was analysed in archived samples from 0-20 cm every second year between 1982 and 2018. Soil quality as assessed by pH, SOC, Ntot, soil microbial biomass C and N, soil basal respiration and alkaline phosphatase activity was measured in the 42nd year of the trial in 0-20 cm samples taken in spring 2019.