Managing classroom behavior is an important prerequisite to effective teaching and a salient need in alternative schools. Unfortunately, students from these schools are often underrepresented in the intervention literature. The primary aim of this study was to compare the effectiveness of two different theoretical approaches to classroom management, one behavioral (i.e., the good behavior game) and the other mindfulness-based (i.e., mindfulness skills training), with a sample of fifth-grade, predominantly African American students from an urban, high-poverty alternative school. The study examined the effectiveness of the two interventions in comparison to each other and a treatment-as-usual control using a quasi-experimental group design with blocked random assignment. Results revealed that neither intervention led to significant improvements in student internalizing behavior, externalizing behavior, or wellbeing. Though, some practically meaningful treatment effects were found through examination of effect sizes. Mindfulness skills training was the only condition to yield meaningful pre-post change in student outcomes, including a moderate therapeutic effect for externalizing behavior and an iatrogenic effect with respect to student wellbeing. These findings provide preliminary evidence that mindfulness skills training might have differential effects on student mental health outcomes, compared with education as usual and a traditional classwide behavioral intervention. Additionally, study findings make clear the importance of careful deliberation when transporting evidence-based interventions to unique student populations and intervention contexts.