The energy and material flows of a city are often described as urban metabolism (UM), which is put forward as a way to link a city’s ecology and economy. UM draws parallels to the biology of individual organisms, yet the analogy is misapplied. In striving to be interdisciplinary, UM makes this organismic comparison rather than identifying the city as an ecosystem, thereby ignoring developments in ecological theory. Using inappropriate rhetoric misdirects researchers, which influences scientific investigation—from problem statements to interpretations. UM is valuable in quantifying the city’s use of natural resources but does not achieve a comprehensive, integrated analysis of the urban ecosystem. To realize an interdisciplinary, perhaps transdisciplinary, understanding of urban ecology, researchers need to emphasize the essential tenets of material flows analysis, view the city as an ecosystem, and use language that properly reflects current knowledge, theory, and conceptual frameworks in the foundational disciplines.