The way we make sense of urban areas stands at a critical point. To reduce energy use in cities, we need to manage the way energy flows into, through and out the city. This paper starts with an overview on energy use at different levels of aggregation which allows us to outline emerging issues on urban metabolism for further research regarding urban energy systems. The research agenda focuses on five aspects: energy services, drivers for energy services, waste, data and dynamic modelling and governance. We give indications regarding the direction we think we should aspire to follow. The variety of themes within urban energy systems demands a coordinated and multidisciplinary research effort to improve our understanding of how the research of urban metabolism can contribute to achieve sustainable development.