The authors analyzed the effects of a multidimensional intervention to promote physical activity (PA) in school, based on self-determination theory. The study involved 88 students, between 14 and 17 years old, who were divided into a control group (n = 59) and an experimental group (n = 29). In the experimental group, a 6-month intervention was conducted, applying a teaching unit of fitness and health in physical education (PE) classes, an extracurricular program of healthy PA, and meetings with families. Questionnaires were administered to measure different motivational variables and PA levels at four time points. Significant differences were found in favor of the experimental group in parental and peer autonomy support; integrated regulation in PE; autonomy, intrinsic, and identified regulation in leisure-time PA; moderate, hard, and very hard PA; and physical self-worth. Motivational effects were maintained over time but the effects on PA levels disappeared at 6 months.