In order to predict the response of carbon (C)-rich soils to external change, models are needed that accurately reflect the conditions of these soils. Here we present an example application of the new Estimation of Carbon in Organic Soils – Sequestration and Emissions (ECOSSE) model to estimate net change in soil C in response to changes in land use in Scotland. The ECOSSE estimate of annual change in soil C stocks for Scotland between 2000 and 2009 is −810 ± 89 kt yr⁻¹, equivalent to 0.037 ± 0.004% yr⁻¹. Increasing the area of land-use change from arable to grass has the greatest potential to sequester soil C, and reducing the area of change from grass to arable has the greatest potential to reduce losses of soil C. Across Scotland, simulated changes in soil C from C-rich soils (C content >6%) between 1950 and 2009 is −63 Mt, compared with −35 Mt from non-C-rich mineral soils; losses from C-rich soils between 2000 and 2009 make up 64% of the total soil C losses. One mitigation option that could be used in upland soils to achieve zero net loss of C from Scottish soils is to stop conversion of semi-natural land to grassland and increase conversion of grassland to seminatural land by 125% relative to the present rate. Mitigation options involving forestry are not included here because the data available to calculate losses of soil C do not account for losses of soil C on drainage of semi-natural land.