Soil organic carbon (SOC) of agricultural soils is observed to decline in many parts of the world. Understanding the reasons behind such losses is important for SOC accounting and formulating climate mitigation strategies. Disentangling the impact of last century’s climate change from effects of preceding land use, management changes and erosion is difficult and most likely impossible to address in observations outside of warming experiments. However, the record of last century’s climate change is available for every part of the globe, so the potential effect of climate change on SOC stocks can be modelled. In this study, an established and validated FAO framework was used to model global agricultural topsoil (0–30 cm) SOC stock dynamics from 1919 to 2018 as attributable to climate change. On average, global agricultural topsoils could have lost 2.5 ± 2.3 Mg C ha−1(3.9 ± 5.4%) with constant net primary production (NPP) or 1.6 ± 3.4 Mg C ha−1(2.5 ± 5.5%) when NPP was considered to be modified by temperature and precipitation. Regional variability could be explained by the complex patterns of changes in temperature and moisture, as well as initial SOC stocks. However, small average SOC losses have been an intrinsic and persistent feature of climate change in all climatic zones. This needs to be taken into consideration in reporting or accounting frameworks and halted in order to mitigate climate change and secure soil health.