The extreme degree of openness of contemporary urban systems with regard to both economy and population creates a serious challenge for the study of urban energy metabolism. A novel tool based on Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM) is proposed to overcome these challenges. It consists of an end-use matrix, a coherent multi-level integrated characterization of the uses of different forms of energy carriers (electricity, heat, fuels) for the various tasks performed in the city, including private and public mobility, tourism, commercial and residential activities. The end-use matrix integrates quantitative data referring to different dimensions (i.e. energy, human activity, land use, value added) and hierarchical (economic sectors and functional elements at lower levels) and spatial scales (i.e. individual buildings, neighborhoods, and the city as a whole). The end-use matrix provides information on both extensive (flows) and intensive variables (flow/fund ratios or benchmarks). Benchmarks are important for policy-making and allow a meaningful comparison of energy performance across hierarchical levels within the urban system, and among different urban systems. The approach is illustrated for Barcelona, a global city characterized by an important service sector.