Sustainability science analyses society-nature interaction on a variety of spatial and temporal scales. By explaining the link between sustainability and socio-economic material and energy flows as well as with colonization of ecosystems, this paper introduces a conceptual framework for empirical applications featured in other contributions to this special issue. The paper discusses how the proposed material and energy flow accounting (MEFA) framework supports such analyses. This framework is an integrated toolbox to account for socio-economic metabolism and colonization of natural processes; above all, land use. We argue that, even though it is at present impossible to define precision sustainability thresholds with respect to many material and energy flows, the MEFA framework is a valuable tool because it tracks these flows in a consistent manner for regions of any scale over time.