In a recent publication (Bahers et al., 2020), we have shown that port cities are particularly interesting territories for studying urban metabolism. Transited through these port cities, flows of goods and energy are very important that cross the oceans to the regions concerned, causing a chain of pollution that extends local emissions through distribution and consumption, but also through ocean pollution related to transportation. Our approach contributes to the emerging field of “political-industrial ecology” (Newell and Cousins, 2015), whose objective is to combine prescriptive and critical results in energy studies (Baka, 2017). From a methodological and empirical point of view, it provides a framework to track the quantities of resource flows across space and time and to study social and environmental dynamics that reveal indirect flows of imports. Therefore we will discuss the dependency on a distant hinterland, the waste-biomass-energy nexus and the metabolic links of power relationship and conflict. We will also analyze the role of metabolic infrastructures, especially the ones oriented towards the so-called renewable (waste-to-energy and biomass). Indeed, it is not enough for an infrastructure to claim renewable energy-based operations to avoid metabolic conflicts (e.g. a biomass thermal power plant and waste-to-energy plant). The urban energy metabolism of the port cities of Nantes-Saint-Nazaire (France) and Gothenburg (in Sweden) will be compared to explore this issue.