The social and ecological impacts of urbanization require integrated management of cities and their resource metabolism for long-term sustainability and economic prosperity. Traditionally, network models are used to study internal metabolic processes in cities, complementing the traditional “black box” urban models to account for the input of material and energy resources and the output of final products and wastes. This study introduces a multi-criteria assessment framework by integrating a unique hybrid-unit input-output model with the emergy accounting method to estimate the environmental support provided to urban socio-economic systems, applied here to the case of Vienna, Austria. By focusing on the internal organisation and functioning of urban socio-economic systems, the proposed framework strengthens the understanding of ecological and socio-economic flows exchanged among industries and the environment. The results suggest that resources can be saved by applying supply-side and demand-side interventions and improving share of renewables. The multi-criteria assessment framework developed in this study allows to investigate the urban metabolism of cities and regional contexts through the identification of sustainable pathways rooted in material circularity and resource efficiency, supporting the design of policies in line with the “integrated wealth assessment” and “circular economy” principles.