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This longitudinal study uses multilevel modeling to examine associations between four autonomy affecting factors and student intrinsic motivation across a school year. Participants were 1055 fifth and sixth graders in 58 classrooms in fall and 974 students in 55 classrooms in spring. Students came from diverse ethnic and economic backgrounds. Results indicate that students’ individual perceptions of autonomy supportive teacher practices are positively related to intrinsic motivation, while perceptions of controlling practices negatively associate with intrinsic motivation. However, associations between classroom autonomy affecting factors and intrinsic motivation diminishes from fall to spring. Findings demonstrate the importance of meeting students’ individual autonomy needs while highlighting differences in how students’ classroom environments affect their intrinsic motivation within a school year.