This paper takes a Long-Term Socio-Ecological Research (LTSER) perspective to integrate important aspects of social inequality into Socio-Ecological Metabolism (SEM) research. SEM has dealt with biophysical features of pre-industrial agricultural systems from a largely apolitical perspective, neglecting social relations and conditions of peasant production and reproduction. One of the politically and economically most important manorial systems in Early Modern Austria (Grundherrschaft Grafenegg) serves as a case study to reconstruct the unequal distribution of central resources between ruling landlords and subjected peasants. We show that peasant land use systems generated small surpluses only, whereas landlords enjoyed significant economies of scale. Furthermore, we explore what these conditions of landlord surplus and peasant scarcity implied for their respective agro-ecological sustainability. Finally, we argue that within pre-industrial agrarian systems sustainability costs of inequality were severely limiting margins for agricultural intensification and growth of peasant economies.