BackgroundSchool safety is fundamental to fostering positive outcomes for children. Violence remains a critical public health issue with 8.1% of elementary and 21.8% of middle school students reporting daily or weekly bullying in 2015–16. Similarly, over half of lifetime mental health concerns become evident before age 14. Thus, elementary school is a key time for comprehensive school safety interventions. Yet, interventions are rarely delivered with fidelity in community settings. Evidence-based interventions must be complemented by implementation strategies to achieve desired public health outcomes.MethodsWe develop and test an intervention focused on promoting a positive school climate guided by a school-based 3-person leadership team (3-PLT) using a hybrid Type II design. The 3-PLT includes a School Resource Officer, (SRO), administrator and mental health services professional as a newly appointed climate specialist (CS). The interventions to be delivered include 1) Restorative justice, 2) Mental Health First Aid and 3) Crime Prevention Through Environmental Design. The CS will lead the team and coordinate implementation through a process of interactive problem solving and supports, consistent with the implementation facilitation strategy. We will conduct a cluster randomized controlled trial with staged entry over two school years in Genesee County, Michigan (n = 20 elementary schools, with 10 participating per school year). We will use a combination of data sources including data collected by schools (e.g., discipline data), a student survey, and a teacher survey. We will also conduct a process evaluation and assess implementation and sustainability through focus groups with key stakeholders, teachers, and students. Finally, we will conduct a cost-benefit analysis.DiscussionResults from both the behavioral outcome and implementation strategy evaluations are expected to have significant implications for school safety and student well-being. This study adopts a unique approach by integrating three evidence-based programs and incorporating implementation facilitation led by the CS as part of the 3-PLT to support intervention delivery and enhance public health impact among schools in disadvantaged communities with students at risk of poor health outcomes. This study aims to create a comprehensive, well-integrated model intervention that is sustainable and can be translated to similar high-risk settings.Trial registrationTrial was retrospectively registered, registration ISRCTN1226421, May 16, 2019.