The purpose of this study was to examine individual- and classroom-level differences in the longitudinal change in motivational regulations during physical education students’ transition from elementary (Grade 6) across middle school (Grades 7 to 9). A sample of 757 Finnish adolescents (M = 12.71, SD = 0.23) participated in this study. Participants of the study responded to questionnaires collected six times. A multilevel latent growth modelling approach was used to analyze the data. Results showed that motivational regulations in physical education developed at different rates during middle school. More specifically, students’: (a) identified regulation increased across Grades 6 to 9; (b) amotivation increased during middle school transition from Grade 6 to 7; and (c) introjected regulation declined from Grade 8 to 9. Other motivational regulations remained stable across time. The changes in amotivation and introjected regulation were largely due to individual factors, whereas the changes in identified regulation were due to environmental factors.