Soils underpin our existence through food production and represent the largest terrestrial carbon store. Understanding soil state-and-change in response to climate and land use change is a major challenge. Our aim is to bridge the science-policy interface by developing a natural capital accounting structure for soil, for example, attempting a mass balance between soil erosion and production, which indicates that barren land, and woody crop areas are most vulnerable to potential soil loss. We test out our approach using earth observation, modelling and ground based sample data from the European Union’s Land Use/Cover Area frame statistical Survey (LUCAS) soil monitoring program. Using land cover change data for 2000–2012 we are able to identify land covers susceptible to change, and the soil resources most at risk. Tree covered soils are associated with the highest carbon stocks, and are on the increase, while areas of arable crops are declining, but artificial surfaces are increasing. The framework developed offers a substantial step forward, demonstrating the development of biophysical soil accounts that can be used in wider socio-economic and policy assessment; initiating the development of an integrated soil monitoring approach called for by the United Nations Intergovernmental Technical Panel on Soils.