Recent decades have seen an expanding literature exploring urban energy and material flows, loosely branded as urban metabolism analysis. However, this has occurred largely in parallel to the mainstream studies of cities as ecosystems. This paper aims to conceptually bridge these two distinctive fields of research, by (a) identifying the common aspects between them; (b) identifying key characteristics of urban ecosystems that can be derived from energy and material flow analysis, namely energy and material budget and pathways; flow intensity; energy and material efficiency; rate of resource depletion, accumulation and transformation; self-sufficiency or external dependency; intra-system heterogeneity; intersystem and temporal variation; and regulating mechanism and governing capacity. I argue that significant ecological insight can be, or has the potential to be, drawn from the rich and rapidly growing empirical findings of urban metabolism studies to understand the behaviour of cities as human-dominated, complex systems. A closer intellectual linkage and cross pollination between urban metabolism and urban ecosystem studies will advance our scientific understanding and better inform urban policy and management practices.