A mixed methods design was employed to investigate the effects of integrated physical activity in academic subjects on high school students’ motivation and well-being over an eight-week period. 87 students in the intervention group and 80 students in the control group completed quantitative questionnaires and eight students in the intervention group took part in qualitative interviews. In the questionnaires and interviews, Self-Determination Theory and the Hierarchical Model of Intrinsic and Extrinsic Motivation constituted the theoretical perspective on motivation, while a hedonic perspective on well-being was used. This study showed that integrated physical activity had a long-term effect on students’ perceived relatedness in academic subjects in that the integrated physical activities brought them closer together. The study further demonstrated that integrated physical activity had short-term effects on students’ perceived autonomy, positive feelings, and negative feelings in academic subjects in that the integrated physical activities were experienced as varying and different. No effects on perceived competence were found.