Limited evidence is available regarding the association of methyl donor nutrients and adolescents’ metabolic health. Therefore, we investigated the relation between a combination of methyl donor nutrients and metabolic health status of overweight and obese Iranian adolescents. In this cross-sectional study, 203 overweight/obese adolescents were included, using a multistage cluster random-sampling method. Dietary intakes were assessed by a validated food frequency questionnaire. Methyl donor nutrient score (MDNS) was constructed based on deciles of vitamins B2, B6, B9, B12, methionine, choline and betaine. Glycemic profile, lipid profile, blood pressure and anthropometric indices were collected. Participants were classified as metabolically healthy obese or unhealthy obese (MUO) based on International Diabetes Federation (IDF) and IDF/Homeostasis Model Assessment Insulin Resistance (HOMA-IR) definitions. Mean age of adolescents was 13.98 $$\pm$$
±
1.61 y and 50.2% of them was girls. After controlling all of the confounders, individuals in the top tertile of MDNS, had lower odds of MUO (OR 0.36; 95% CI 0.13–0.95) according to IFD criteria. Considering IDF/HOMA-IR criteria, an inverse marginally significant association was observed between the highest tertile of MDNS and odds of MUO (OR 0.36; 95% CI 0.12–1.02) in the fully-adjusted model. Furthermore, significant inverse association was found between each unit increase in MDNS and odds of MUO based on IDF criteria, but not for IDF/HOMA-IR definition. We found that overweight/obese adolescents with higher dietary intakes of methyl donor nutrients were less likely to be metabolically unhealthy. Further studies are needed to confirm the findings.