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This mixed method study investigates the contextual and personal factors that contribute to momentary fluctuation and long term change in children’s behavioral engagement and affect during a six-week intervention, between classrooms employing either Direct Instruction or Collaborative Group work. A total of 96 four-minute video clips from 24 fifth-grade classrooms were coded, and student behavioral engagement, affect, and lesson participation type were examined from the thirty-two 30-second intervals for each of 150 children. Results showed that classroom instructional approach influenced children’s affect, and moderated the impact of children’s participation type on their behavioral engagement. Children’s engagement and positive affect aggregated over the intervention significantly predicted knowledge acquired during the intervention.