Urban policy makers and researchers consistently recognize the challenge of more effectively reshaping the linkages between cities, urban infrastructure, ecosystem services, and natural resources. The aim of this article is to consider the potential value of developing connections between two currently disconnected approaches to resource use and cities—material flow analysis (MFA) and transitions analysis (TA). This article attempts to address this deficit and looks critically at resource flows through cities and the infrastructures that have been—or could be—reconfigured to more effectively manage these flows from the perspectives of MFA and TA. This is an issue that has not been addressed, with the result that inadequate attention has been paid to the reconfiguring of urban infrastructures whose construction and maintenance are, in turn, often the largest expenditures at the city government level. Insufficient attention has been given to the fact that the design, construction, and operation of infrastructures (specifically energy, waste, water, sanitation, and transport infrastructures) create a sociotechnical environment that plays an important role in shaping, and potentially reshaping, how resources are procured, used, and disposed of by the city. The challenge, of course, is how such a transition takes place, who leads it and what social and governance processes are best suited to facilitate such city transitions. This article assesses the role of MFA and TA in understanding these resource flows and urban infrastructures, making it possible to begin to tackle this challenge in practical transformative ways.