We describe the development and application of an integrated data and modelling system for estimating soil carbon (C) fluxes from mineral soils caused by changes in climate, land use and land management at 1-km resolution in the UK (RothCUK). The system was developed with the aim of improving methods for United Nations Framework Convention on Climate Change (UNFCCC) and Kyoto Protocol accounting and integrates national scale data sets of soil properties, land use and climate with the Rothamsted carbon model (RothC). A preliminary estimate of soil C fluxes because of land use change (LUC) over the period 1990–2000 is presented as an example application of the system. RothCUK shows LUC to be a net source of CO2 from 1990 to 2000 although the RothC estimate was smaller (6488 kt C) than the estimate from the single exponential model (SEM) method currently used to calculate C fluxes due to LUC for the UK National Greenhouse Gas Inventory (mean: 9412 kt C). Based on previous studies, an uncertainty range in our estimates of ±50–100% seems plausible. In agreement with the SEM, RothCUK suggests that the largest single contributor to soil C fluxes from LUC was conversion of grassland to arable land. Differences between the results may be attributed to differences in the two models and the assumptions and underlying data used in making the calculations. The RothCUK system provides a powerful method for estimating changes in soil C stocks, enabling areas and management systems with particularly large changes in soil C stocks to be located at fine resolution.