Many ecosystem models incorrectly treat urban areas as devoid of vegetation and biogenic carbon (C) fluxes. We sought to improve estimates of urban biomass and biogenic C fluxes using existing, nationally available data products. We characterized biogenic influence on urban C cycling throughout Massachusetts, USA using an ecosystem model that integrates improved representation of urban vegetation, growing conditions associated with urban heat island (UHI), and altered urban phenology. Boston's biomass density is 1/4 that of rural forests, however 87% of Massachusetts' urban landscape is vegetated. Model results suggest that, kilogram-for-kilogram, urban vegetation cycles C twice as fast as rural forests. Urban vegetation releases (RE) and absorbs (GEE) the equivalent of 11 and 14%, respectively, of anthropogenic emissions in the most urban portions of the state. While urban vegetation in Massachusetts fully sequesters anthropogenic emissions from smaller cities in the region, Boston's UHI reduces annual C storage by > 20% such that vegetation offsets only 2% of anthropogenic emissions. Asynchrony between temporal patterns of biogenic and anthropogenic C fluxes further constrains the emissions mitigation potential of urban vegetation. However, neglecting to account for biogenic C fluxes in cities can impair efforts to accurately monitor, report, verify, and reduce anthropogenic emissions.