Methodology is developed for linking the urban metabolism (UM) to global environmental stresses on the carbon (C) cycle, nitrogen (N) cycle, and biodiversity loss. UM variables are systematically mapped to the drivers of carbon, nitrogen, and biodiversity impacts. Change in mean species abundance is used as metric of biodiversity loss, by adopting the dose-response relationships from the GLOBIO model. The main biodiversity drivers related to UM included here are land-use change (LUC) and atmospheric N deposition. The methodology is demonstrated by studying the nexus for Shanghai in 2006, based on energy and soybean consumption. Results for Shanghai show a strong nexus between C, N, and biodiversity impact due to electricity consumption and energy used in manufacturing industries and construction. Prioritization of the shift away from coal energy will therefore lead to lowering the urban growth impact on all three dimensions. Road transportation, domestic aviation, and the metal industry impact only the C footprint highly, whereas district energy impacts only biodiversity loss highly, showing a weak nexus. Among the global impacts of soybean consumption in Shanghai on biodiversity loss (due to LUC only), the highest impact occurs in Uruguay (0.52%) followed by Brazil (0.05%) and Argentina (0.02%). The local impact on biodiversity loss (i.e., within China) of soybean consumption in Shanghai is 1.03%. However, the methodology and results are limited due to the partial inclusion of drivers, a carbon footprint based on carbon dioxide emissions only, and limitations of biodiversity loss models. Potential to overcome methodological limitations is discussed.