Abstract Objective: Using newly harmonised individual-level data on health and socio-economic environments in Latin American cities (from the Salud Urbana en América Latina (SALURBAL) study), we assessed the association between obesity and education levels and explored potential effect modification of this association by city-level socio-economic development. Design: This cross-sectional study used survey data collected between 2002 and 2017. Absolute and relative educational inequalities in obesity (BMI ≥ 30 kg/m2, derived from measured weight and height) were calculated first. Then, a two-level mixed-effects logistic regression was run to test for effect modification of the education–obesity association by city-level socio-economic development. All analyses were stratified by sex. Setting: One hundred seventy-six Latin American cities within eight countries (Brazil, Chile, Colombia, Costa Rica, El Salvador, Guatemala, Mexico and Peru). Participants: 53 186 adults aged >18 years old. Results: Among women, 25 % were living with obesity and obesity was negatively associated with educational level (higher education–lower obesity) and this pattern was consistent across city-level socio-economic development. Among men, 18 % were living with obesity and there was a positive association between education and obesity (higher education–higher obesity) for men living in cities with lower levels of development, whereas for those living in cities with higher levels of development, the pattern was inverted and university education was protective of obesity. Conclusions: Among women, education was protective of obesity regardless, whereas among men, it was only protective in cities with higher levels of development. These divergent results suggest the need for sex- and city-specific interventions to reduce obesity prevalence and inequalities.