<b><i>Background/Aims:</i></b> In adolescents, overweight and obesity are associated with an increased cardiovascular risk. The aim of this study was to determine the impact of a school-based nutritional education program (NEP) on lifestyle changes in Spanish adolescents. <b><i>Methods:</i></b> We selected 263 secondary school students (127 males) aged 12–16 years from Granada (Spain), who were followed up throughout 1 school year (2009–2010). At the beginning and end of the school year, data were gathered on the food consumption frequency, and anthropometric and biochemical profile. The NEP comprised a class on nutritional recommendations every 15 days, and administration of a daily breakfast of 275–350 kcal. <b><i>Results:</i></b> After the intervention, the prevalence of overweight and obesity decreased among both male and female students (p < 0.001) and there was also a global reduction in the prevalence of the metabolic syndrome (MS) from 32.2 to 19.7% (p < 0.001); in addition, body mass index was significantly decreased in normal weight, overweight and obesity groups (p = 0.001 and p = 0.02, respectively), and high-density-lipoprotein cholesterol and lean body mass was increased in all groups (p = 0.001). <b><i>Conclusion:</i></b> The NEP achieved a medium-term reduction in the prevalence of overweight and obesity and had a significant and positive effect on MS components in all groups.