Most university students do not follow recommendations for fruit and vegetable intake, with a consequent increase in the prevalence of cardiovascular disease (CVD) risk factors. The aim of this study was to compare obesity prevalence and biomarkers of metabolic status between Italian and Spanish university students, in relation with the consumption of fruits and vegetables. Food consumption, adherence to a Mediterranean diet (MD), level of physical activity (PA), blood glucose, total cholesterol, triglycerides and ketones, blood pressure, and body composition were evaluated. Among CVD risk factors, only glucose was significantly higher in Spaniards (SP), and only 3.1% of SP presented ketosis. SP had a higher percentage of energy from fat. Although adherence to MD and fruit and vegetable consumption did not differ between Italians and SP, students who consumed at least four servings of fruit and vegetables (FV group) showed better values for pressure and metabolic parameters than the no FV group. We observed an association between consumption of fruit and PA. Students who consumed more vegetables than fruit reported a better body composition profile and lower glucose concentrations. As previously suggested, in addition to PA, two servings of fruit and three servings of vegetables per day should be recommended.