Introduction: The Mediterranean diet (MD) is widely known as a healthy eating pattern for preventing and reducing childhood obesity. School has been described as a privileged setting for modulating eating habits and health promotion. Objective: The study aimed to analyse the effects of a nutrition education programme on the nutritional status and MD adherence in children and adolescents from São Miguel Island, Azores. Methods: A total of 298 students from the 1st to the 3rd cycle were included. An anthropometric assessment (height, weight, and waist circumference) was performed, and participants completed a questionnaire which included KIDMED Index at baseline and after the intervention. This programme had grade-appropriate nutritional education activities, promoting the Mediterranean food pattern. Results: After the intervention, students with a higher education level showed improvements in nutritional status. We verified an increase in the obesity prevalence in 1st cycle students (26.7% vs 32.2%) and a decrease in the 2nd and 3rd cycles (26.4% vs 20.7% and 21.5% vs 20.7%, respectively). Concerning to KIDMED index, in 1st cycle students, we observed a decrease in the percentage of optimal adherence (52.2% vs 47.8%). Otherwise, in 2nd and 3rd cycles, students enhanced their optimal MD adherence (31.0% vs 35.6% and 27.3% vs 30.6%, respectively). It was found a negatively correlation between MD adherence and body mass index (RS = - 0.154, p = 0.010) and between MD adherence and waist circumference (RS = - 0.138, p = 0.021). Conclusion: Our findings suggest that a nutrition education programme is more effective in improving nutritional status and MD adherence in adolescents, compared with children.