In this paper we examine two central concepts of urban metabolism (‘system boundaries' and ‘flows'), and explore how to approach them as a means to politicise urban metabolism research. We present empirical findings from two case studies of waste management, in Mexico City and Santiago de Chile, looking at: the materiality of waste flows, the actors involved in them, and how waste flows relate to issues of environmental justice. We argue that urban metabolism, as a methodology to understand urban sustainability, has the potential to produce knowledge to trigger urban transformations, and to analyse the social, political and environmental aspects of waste management in urban areas.