Background: Metabolic health in people with obesity is determined by body composition. In this study, we examined the influence of a combined strength exercise and motivational programme –embedded in the school curriculum– on adolescents body composition and daily physical activity. Methods: A total of 695 adolescents (11-15y) from nine Dutch secondary schools participated in a one year cluster randomised controlled trial (RCT). In the intervention schools, physical education teachers were instructed to spend 15–30 min of all physical education lessons (2× per week) on strength exercises. Monthly motivational lessons were given to stimulate students to be more physically active. Control schools followed their usual curriculum. The primary outcome measure was body composition assessed by the deuterium dilution technique. Daily physical activity and sedentary behaviour measured by accelerometry served as a secondary outcome. Results: After 1 year, a 1.6% fat mass difference was found in favour of the intervention group (p = .007). This reflected a 0.9 kg difference in fat free mass (intervention>control; p = .041) and 0.7 kg difference in fat mass (intervention<control; p = .054). Daily physical activity decreased from baseline to posttest in both groups, but less so in the intervention group (p = .049). After 1 year, a difference of 0.4% was found for moderate to vigorous physical activities in favour of the intervention group (p = .046). No differences in sedentary behaviour, or light physical activity were found between groups. Conclusion: In 11–15 year olds, the combination of strength exercises plus motivational lessons contributed to an improvement in body composition and a smaller decrease in physical activity level.