To predict the response of C-rich soils to external change, models are needed that accurately reflect the conditions of these soils. Estimation of Carbon in Organic Soils—Sequestration and Emissions (ECOSSE) is a model that allows simulations of soil C and N turnover in both mineral and organic soils using only the limited meteorological, land-use and soil data that is available at the national scale. Because it is able to function at field as well as national scales if appropriate input data are used, field-scale evaluations can be used to determine uncertainty in national simulations. Here we present an evaluation of the uncertainty expected in national-scale simulations of Scotland, using data from the National Soil Inventory of Scotland. This data set provides measurements of C change for the range of soils, climates and land-use types found across Scotland. The simulated values show a high degree of association with the measurements in both total C and change in C content of the soil. Over all sites where land-use change occurred, the average deviation between the simulated and measured values of percentage change in soil C was less than the experimental error (11% simulation error, 53% measurement error). This suggests that the uncertainty in the national-scale simulations will be ~11%. Only a small bias in the simulations was observed compared to the measured values, suggesting that a small underestimate of the change in soil C should be expected at the national scale (–4%).