Based on Self-Determination Theory (Deci & Ryan, 2000), this study tested whether changes in autonomous motivation toward physical education (AMPE) during the transition from elementary to secondary school can be predicted by changes in perceived need support from the physical education (PE) teacher and perceived physical school environment. Self-reported data were gathered from 472 Flemish (northern part of Belgium) students in 6th grade (2009) and again in 8th grade (2011). Mediation analyses showed that an increase in perceived need support from the PE teacher was related to an increase in AMPE (boys: ß = 0.42; girls: ß = 0.50). In boys, this relation was mediated by changes in perceived competence (ß = 0.08). In girls, this relation was mediated by changes in perceived autonomy (ß = 0.12), perceived competence (ß = 0.14), and perceived relatedness (ß = 0.05). This study shows that PE teachers should be need-supportive to maintain a good quality of motivation in students.