Changes in soil organic carbon (SOC) storage in agricultural land are an important part of the Land Use, Land‐Use Change and Forestry component of national greenhouse gas emission inventories. Furthermore, as climate mitigation strategies and incentives for carbon farming are being developed, accurate estimates of SOC stocks are essential to verify any management‐induced changes in SOC. Based on agricultural mineral soils in the Danish soil‐monitoring network, we analysed management effects on SOC stocks using data from the two most recent surveys (2009 and 2019). Between 2009 and 2019, the average increase in SOC stock was 1.2 Mg C ha−1 for 0–50 cm despite a loss of 1.2 Mg C ha−1 from the topsoil (0–25 cm), stressing the importance of including deeper soil layers in soil‐monitoring networks. Comparing all four national surveys (1986, 1997, 2009, 2019), the mean SOC stock of mineral soils in Denmark appears stable. The change in SOC stock between 2009 and 2019 was analysed in detail in relation to management practices as reported by farmers. We found that the effects of single management factors were difficult to isolate from co‐varying factors including soil parameters and that the use of farm management data to explain changes in SOC stocks observed in soil‐monitoring networks appears limited. Uncertainty in SOC stock estimates also arises from low sampling frequency and statistical challenges related to regression to the mean. However, repeated stock measurements at decadal intervals still represent a benchmark for the overall development in regional and national SOC storage, as affected by actual farm management.