Soils are the basis of life on land and the ways in which we manage them for crop production, impact their role, functions and quality. Conventional farming uses industrial inputs to a level that is economically justified, whilst organic farming systems avoid mineral fertilizers and synthetic chemical pesticides. This study investigates the long-term effect of organic and conventional farming systems on soil quality. The DOK trial (bioDynamic, bioOrganic, Konventionell (German for conventional)) running since 1978 in Therwil (CH), compares bioorganic (BIOORG), biodynamic (BIODYN), and conventional (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). The treatments in the DOK trial vary in plant protection and receive system-specific organic matter inputs differing in rate and quality. With this work, we revisit the soil organic carbon (SOC) dynamics across 42 years and redefine the previous perception of mainly declining SOC contents after 21 years of organic and conventional management (Fliessbach et al. 2007). After 42 years, we found SOC contents to be increased in BIODYN 1.4 and to a lesser extent also in BIOORG 1.4. CONFYM 1.4 showed stable SOC contents, while systems fertilized with manure of 0.7 livestock units and CONMIN lost SOC. SOC loss was highest in NOFERT. Enhanced biological soil quality under organic and particularly biodynamic management highlights the close link between soil biology and SOC changes. The impact of farming systems on SOC was detectable after 2 decades of continuous management. We conclude that recycling manure at a level of 1.4 livestock units per hectare permits maintenance of SOC levels and that composting manure, as performed in BIODYN 1.4, helps to further increase SOC levels and improve biological soil quality.