We applied the trans-contextual model (TCM) to examine the effects of middle school students’ perceived autonomy support from their physical education (PE) teachers on autonomous motivation toward PE in school and, critically, autonomous motivation toward, and actual participation in, leisure-time physical activity (PA). The research adopted a three-wave prospective design enabling the modeling of change in the TCM constructs over time. Middle school students (N = 248) aged from 12 to 16 years reported their perceived autonomy support, autonomous motivation in PE, autonomous motivation toward leisure-time PA, attitudes, subjective norms, perceived behavioral control (PBC), intentions for PA in leisure-time, and leisure-time PA participation. The psychological constructs and leisure-time PA were measured at baseline (T0) and at a first follow-up occasion (T1) 5 weeks later. Another measure of PA was taken at a second follow-up occasion (T2) a further 5 weeks later. A single-indicator structural equation model using residualized change scores revealed that perceived autonomy support predicted autonomous motivation in PE (β =.345), and autonomous motivation in PE predicted autonomous motivation for leisure-time PA (β =.484). Autonomous motivation toward leisure-time PA predicted attitudes (β =.425), subjective norms (β =.264), and PBC (β =.517). Autonomous motivation toward leisure-time PA (β =.376), attitude (β =.231), and subjective norms (β =.185) predicted intentions toward leisure-time PA, and intentions predicted PA (β =.198). Findings extend research on the TCM by demonstrating its efficacy in predicting change in middle school students’ autonomous motivation across PE and leisure-time contexts, and accounting for change in intentions toward, and actual participation in, leisure-time PA.