The urbanization trend points out that about 70% of the global population is expected to live in cities by 2050, occupying more land and generating more emissions. The environmental impacts generated by urban systems can affect the capacity of natural ecosystems to provide ecosystem goods and services vital for human health and well-being. Therefore, the sustainable management of urban systems is crucial for ensuring the long-term sustainability of the human economy. Management strategies should be based on the “urban metabolism” perspective, considering cities as socio-ecological systems characterized by complex human-nature interactions. This perspective is based on a shift from traditional “black box” urban models, accounting for the input of material and energy resources, and the output of final products (i.e., generated GDP and supported population) and waste, to network models capable of unfolding the internal metabolism of cities. In this study, we propose a multicriteria assessment framework integrating the energy input-output and the emergy accounting models for a comprehensive understanding of urban systems metabolism. In particular, this framework accounts for both environmental and socio-economic flows exchanged between industrial sectors and the environment, focusing on the internal organization and functioning of urban systems. The proposed multi-criteria and system-based approach for studying urban systems can support local managers and policymakers in charge of developing environmental policies based on the "integrated wealth assessment" and “circular economy” principles.