Given the importance of soil organic carbon (SOC) as a pool in the global carbon cycle and an indicator for soil quality, there exits an urgent need to monitor this dynamic soil property. Here, we present a modelling approach to analyze the spatial patterns and temporal evolution of organic carbon in mineral soils under agricultural land use in Belgium. An empirical model, predicting the SOC concentration in the top 0.3 m, as a function of precipitation, land use, soil type and management has been constructed and applied within a spatial context using data from different time slices. The results show that SOC content is strongly correlated with precipitation and temperature under cropland and with texture and drainage under grassland. Total SOC stock increased with 1.3% from 6.18 ± 0.03 kg C m−2 in 1960 to 6.26 ± 0.07 kg C m−2 in 2006. Although this increase was not significant (P>0.05), a significant discrepancy between cropland (−8%) and grassland (+10%) was observed. Foremost, the grasslands in the hilly southern part of the country, under relatively wet climate conditions, acted as important sinks of CO2. Under cropland, all soil types were characterized by a decrease in SOC, except for the clay soils in the north-west. Currently, croplands in the central loam region have SOC concentrations close to 10 g C kg−1 indicating that these soils are at risk of a decline in aggregate stability. An overall strong SOC decline in poorly drained soils is probably caused by artificial drainage. Further research is needed to gain more insight into the processes driving the observed SOC trends. Moreover, the use of updated drainage class information and land management history would improve the empirical models.