Purpose To examine the adherence to the Mediterranean dietary pattern (MDP) in metabolically healthy overweight or obese (MHO) and metabolically unhealthy obese (MUO) European adolescents. Methods In this cross-sectional study, 137 overweight/obese adolescents aged 12-17 years old from the HELENA study were included. Height, weight, waist circumference and skinfold thickness were measured and body mass index and body fat percent were calculated. Systolic and diastolic blood pressure, glucose, HDL cholesterol, triglycerides and cardiorespiratory fitness (20 m shuttle run test) were measured. MHO and MUO phenotypes were categorized following the Jolliffe and Janssen criteria. Two non-consecutive 24 h recalls were used for dietary intake assessment and the adherence to the MDP was calculated using the Mediterranean dietary pattern score (MDP score) (range 0-9). Results A total of 45 (22 girls) adolescents (32.8%) were categorized as MHO. The adherence to the MDP was significantly higher in MHO than in MUO adolescents regardless of age, sex, body fat percentage, energy intake and center (MDP score: 4.6 +/- 1.6 vs. 3.9 +/- 1.5, p = 0.036), but this difference became non-significant after further adjustment for cardiorespiratory fitness. Participants who had a low adherence to the MDP (MDP score <= 4) had a higher likelihood of having MUO phenotype regardless of sex, age, energy intake, center and body fat percentage (OR 2.2; 95% CI 1.01-4.81, p = 0.048). Conclusions Adherence to the MDP might be beneficial to maintain metabolic health in overweight/obese adolescents, yet cardiorespiratory fitness seems to play a key role on the metabolic phenotype.