Background: Evidence shows that the relationship between physical activity and mental wellbeing varies across different life domains. However, little is known about the reasons for such variation. We aimed to explore motivation as a potential underlying factor that may explain some of the variation, by qualitatively examining adolescents’ physical activity experiences and perceived affective outcomes during leisure-time, active travel, and physical education. Method: We conducted computer-assisted-self-interviews with 144 adolescents (M age = 14.42 years) about physical activity experiences they believed led to positive and negative affect. The participants were asked when the activities occurred, their reason for participation, and with whom they participated. Participants also responded to questions specifically about leisure-time, active travel, and physical education. Results: Thematic analysis revealed that adolescents perceived leisure-time physical activity led to positive affect, because it was fun, increased self-esteem, and provided a sense of belonging. However, active travel was associated with positive affect among those who participated for enjoyment or health benefits, far more than those who participated because it was their only means of transportation. Similarly, those who believed physical education was fun, and experienced a sense of belonging, were more likely to report it led to positive affect, compared to those who participated in physical education because they were forced. Conclusions: Compared to other life domains, more adolescents associate leisure-time physical activity with positive affect. However, promoting more autonomous motivation may enhance the effect of physical activity on wellbeing in other domains, such as active travel and physical education.