Effective approaches to promote adolescent physical activity are needed. Moreover, a one-size-fits-all approach has been minimally successful to date. This randomized controlled trial evaluates a theory-based personalized exercise prescription to enhance motivation for being active and physical activity participation among adolescent reluctant exercisers. Adolescents were characterized by affective style as reluctant (predisposed to negative affect during exercise) or latent (predisposed to positive affect during exercise) exercisers based on their affective response to an acute exercise task, and then randomly assigned to an exercise prescription of either a personalized or a moderate intensity. Assignment was double-blind. Assessments were pre- and post- the 8-week intervention. Participants were an ethnically diverse group of adolescents (19 % non-Latino White) in a public middle-school. The exercise intensity manipulation and assessments took place at the school site during regular Physical Education. Participants were assigned to either a moderate-intensity exercise prescription [target heart rate (HR) range 60–80 % of HR max] or a personalized exercise prescription corresponding to an intensity that “feels good” to the individual for 8 weeks during daily Physical Education. Outcome measures included exercise-related intrinsic motivation (via questionnaire), and daily moderate-to-vigorous physical activity (MVPA; via accelerometer). The exercise intensity manipulation did not yield actual differences in exercise intensity during PE, and had no effect on either Intrinsic Motivation or MVPA. There was no significant interaction between affective style and group assignment in predicting Intrinsic Motivation or MVPA. This study did not find support for a link between affective experiences during exercise and physical activity participation. Providing adolescents with a personalized exercise intensity prescription and asking them to follow the prescription during PE was not an effective strategy to manipulate their affective experience of exercise. A more rigorous test of affective manipulation may require supervised exercise sessions during which exercise intensity can be directly observed and controlled.