Latin America is the world’s most urbanized region and its heterogeneous urban development may impact chronic diseases. Here, we evaluated the association of built environment characteristics at the sub-city —intersection density, greenness, and population density— and city-level —fragmentation and isolation— with body mass index (BMI), obesity, and type 2 diabetes (T2D). Data from 93,280 (BMI and obesity) and 122,211 individuals (T2D) was analysed across 10 countries. Living in areas with higher intersection density was positively associated with BMI and obesity, whereas living in more fragmented and greener areas were negatively associated. T2D was positively associated with intersection density, but negatively associated with greenness and population density. The rapid urban expansion experienced by Latin America provides unique insights and vastly expand opportunities for population-wide urban interventions aimed at reducing obesity and T2D burden.