Students with disabilities are at an increased risk of experiencing poorer quality peer relationships than those without disabilities. Previous school-based efforts to promote positive peer interactions among students with and without disabilities have included individual skill development and broader initiatives such as inclusive school practices. In the current study, we investigate the effects of cooperative learning (CL) on peer relationships, peer academic supports, and classroom engagement of middle school students with and without disabilities over two years. Using 4 waves of data from a cluster randomized trial of middle schools, we hypothesized that CL would create positive gains in study outcomes among all students, but we anticipated that effects would be more pronounced among students with disabilities. Results confirmed these hypotheses and highlighted the potential role of CL in creating greater social integration among students with and without disabilities. The implications of these findings for practitioners and policymakers are discussed.