We study how urban quality evolves as a result of carbon dioxide emissions as urban agglomerations grow. We employ a bottom-up approach combining two unprecedented microscopic data on population and carbon dioxide emissions in the continental US. We first aggregate settlements that are close to each other into cities using the City Clustering Algorithm (CCA) defining cities beyond the administrative boundaries. Then, we use data on CO2 emissions at a fine geographic scale to determine the total emissions of each city. We find a superlinear scaling behavior, expressed by a power-law, between CO2 emissions and city population with average allometric exponent β = 1.46 across all cities in the US. This result suggests that the high productivity of large cities is done at the expense of a proportionally larger amount of emissions compared to small cities. Furthermore, our results are substantially different from those obtained by the standard administrative definition of cities, i.e. Metropolitan Statistical Area (MSA). Specifically, MSAs display isometric scaling emissions and we argue that this discrepancy is due to the overestimation of MSA areas. The results suggest that allometric studies based on administrative boundaries to define cities may suffer from endogeneity bias.