A youth’s ability to adapt during educational transitions has long-term, positive impacts on their academic achievement and mental health. Although supportive relationships with parents, peers, and teachers are protective factors associated with successful educational transitions, little is known about the reciprocal link between the quality of these interpersonal relationships and school well-being, with even less known about how these two constructs affect academic achievement. This longitudinal study examined how the quality of interpersonal relationships and school well-being worked together to affect academic achievement during the transition from primary school to lower secondary school. Data were collected from 848 Finnish adolescents (54% girls, mean age at the outset 12.3 years) over the course of sixth and seventh grade. The results support a transactional model illustrating the reciprocal associations between the quality of interpersonal relationships and school well-being during the transition to lower secondary school. As such, the presence of high quality interpersonal relationships promoted higher academic achievement through increased school well-being, whereas high school well-being promoted higher subsequent academic achievement through increased quality of interpersonal relationships. Overall, the results suggest that promoting learning outcomes and helping adolescents with challenges during educational transitions is a critical part of supporting school well-being and the formation of high-quality interpersonal relationships.