Few studies assess consumer response to nutrition labeling, especially in less-developed countries. We analyzed the link between nutrition labeling and obesity in Ecuador using a representative cross-sectional sample of 29,770 individuals from the National Health and Nutrition Survey (ENSANUT) in 2018. Nutrition labeling reduced the probability of obesity in adolescent (12–18 years old) and adult (18–59 years old) people by 4% (CI: − 5.7, − 2.2) and 8.4% (CI: − 12.7, − 4.0), respectively. The magnitude of average treatment effect of using nutrition label on obesity ranged from 0.90 (CI: − 1.299, − 0.500) to 1 (CI: − 1.355, − 0.645) BMI points for adolescent, and from 1.16 (CI: − 1.554, − 0.766) to 1.80 (CI: − 2.791, − 0.811) BMI points for adult. The effect of nutrition labeling is greater among the less obese. We recommend that health policy makers and clinicians continue to promote nutrition labeling especially where obesity is not chronic, where nutrition labeling is most successful.