Substance use in adolescence is a significant public health issue, particularly in early-to-mid adolescence, which represents a window of risk in the etiology of substance abuse and dependence. Substance use during this development period often results from affiliation with deviant peers, who model, facilitate, and reinforce use. Existing school-based substance use prevention programs have historically aimed to build adolescent knowledge regarding the dangers of substance use and/or enhance peer refusal skills. Research finds that these programs have had some success in reducing substance use, but meta-analyses report that average effect sizes are small. In a small one-year cluster randomized trial (12 middle and high schools; N = 813 students; ClinicalTrials.gov: NCT04478240), cooperative learning (CL) was implemented with the support of specialized technology and evaluated for its ability to reduce deviant peer affiliation and, in turn, reduce substance use. CL is a structured approach to small-group learning that provides at-risk youth with the opportunity to build friendships with more prosocial youth, interrupting the process of deviant peer clustering. Multi-level modeling revealed intervention effects for deviant peer affiliation and alcohol use across the sample, while tobacco use was significantly reduced among non-White students; intervention effects for marijuana use were only marginally significant. Effects for dosage were found for all outcomes, suggesting that every lesson taught had a significant impact. We conclude that CL, delivered with the aid of specialized technology, represents a viable option for universal substance use prevention. Future research should attempt to combine this approach with evidence-based prevention curricula.