This study examined the cross-lagged relationships between students' autonomous motivations (intrinsic motivation and identified regulations) and approach goals (mastery and performance) in school. The sample included 449 students (52% girls) in Grades 7 and 8 (secondary 1 and 2). Results showed that intrinsic motivation (IM) positively predicted approach goals 20 months later, while mastery-approach goals (MAp) positively predicted autonomous motivations. A second objective was to test the contributions of autonomous motivations and approach goals to students' school functioning measured 32 months after the beginning of the study. Five main findings can be highlighted: IM contributed to (1) increased academic achievement (via high MAp and PAp), (2) increased social anxiety (via high PAp), and (3) decreased disruptive behaviours (via high MAp); MAp goals predicted (4) a decreased in disruptive behaviours (via high identified regulation) and (5) increases in achievement (via high IM). Implications for education stakeholders are presented.