The concept of urban metabolism has often been used to model and analyze urban regions to provide insights on their environmental sustainability. However, no consensus exists on the assessment methods that should be used to analyze the sustainability of these complex systems. This lack of consistency prevents data sharing and comparison between most studies. Past and current publications are therefore surveyed to identify key methodological aspects that could be favored to harmonize the sustainability assessment of urban metabolism. This investigation is structured around the common aspects of environmental assessment methods that have been used for the past forty years. It suggests that a network system modeling approach, a global life-cycle perspective, and a multi-criteria assessment are strategic choices for environmental sustainability assessment. While challenging in their implementations, these choices can offer common grounds to capitalize on the knowledge brought forth by new studies. The investigation also discusses basic principles to propose developments like the use of a functional equivalent as a basis of comparison and the use of specific uncertainty assessment methods. These propositions could help to improve the clarity of future studies that tackle the question of environmental sustainability in urban metabolism.