A successful crop rotation choice is key to the profitability and sustainability of farm management and may simultaneously have an impact on soil organic carbon (SOC) content. In this study, we estimated how changes in crop rotations affected SOC balance in Finland between 2009 and 2018, using geospatial data and Bayesian modeling. The area designated for perennial-dominated and diverse cereal rotations increased over the study period. Perennial grassland rotation was found to have a positive impact on SOC balance, while rotations dominated by annual crops did not differ in their impacts on SOC content. At the national scale, changes in Finnish crop rotations resulted in an estimated annual mitigation of the loss of SOC content by 1336 Mg C year−1 in mineral soils and reduced the carbon dioxide emissions of organic soils by 10,475 Mg C year−1. The combined effect of these two contributions is 11,811 Mg C year−1, with an 80% probability interval of (−6600; 30,300) Mg C year−1. While the overall impact of changes in crop rotations on SOC is relatively small, a continued change to more diverse and perennial-dominated crop rotations may have other agronomic and environmental benefits, e.g. on resilience and biodiversity.