Background: Poor dietary habits and low levels of physical activity (PA) have a strong tendency to track from childhood into adulthood. The Mediterranean Diet (MD) is known to be extremely healthy, associated with lower BMI and a lower risk of obesity in children and adolescents. Therefore, adherence to the MD was compared between Spanish (n = 182) and German (n = 152) children aged 10 to 13 years to examine a possible more “westernized” diet in Spain with a non-Mediterranean country, that traditionally prefers a “Western diet” and to determine the association between adherence to the MD and gender, body composition, and PA levels. Methods: In the German observational longitudinal cohort study and the Spanish cohort study, body composition and questionnaires (KIDMED, Diet Quality (IAES)) were obtained, and accelerometers (Actigraph) were applied to detect PA. Results: Girls had higher BMI-standard deviation score (SDS) than boys and Spanish girls were less active than boys. Differences were detected in MD habits, such as favorable fruit-, vegetables-, fish-intakes, and dairy products in Spanish children and unfavorable consumptions of fast food, processed bakery goods, candies, and sweet beverages in German children. Independently of country, girls, children with lower BMI-SDS and children with higher PA level were related with better diet quality. Conclusion: Spanish children showed higher adherence to MD and diet quality (IAES) compared to German children, but there was a trend toward a more “westernized” diet. Gender, body composition, and PA influenced nutrition regardless of country.