BackgroundThis paper describes the study protocol of a hybrid type I randomized controlled trial that evaluates the effectiveness and cost-effectiveness of implementing Empowering African-American Women on the Road to Health (E-WORTH), an Afrocentric, group-based, computerized human immunodeficiency virus (HIV)/sexually transmitted infection (STI) prevention intervention for controlled substance-using black women in community corrections settings in New York City.Methods/designWe provide an overview of E-WORTH’s hybrid type I design, which is guided by the Consolidated Framework for Implementation Research (CFIR). E-WORTH combines HIV/STI and intimate partner violence (IPV) prevention components and tests the comparative effectiveness of E-WORTH and streamlined HIV testing versus streamlined HIV testing alone in decreasing biologically confirmed HIV and STI incidence, sexual risk, and IPV, as well as in improving access to HIV and STI prevention services and care.DiscussionThis paper provides an overview of E-WORTH’s intervention protocol and serves as a framework for using hybrid type I designs, guided by the CFIR conceptual framework, to evaluate HIV/STI and IPV prevention interventions in community corrections settings. We discuss how E-WORTH’s hybrid type I design advances implementation science through its effectiveness and cost-effectiveness aims as well as through a mixed-methods study that evaluates multilevel theory-driven factors (structural, organizational, staffing, and client) guided by the CFIR that influences the implementation of E-WORTH in a criminal justice setting. This study also addresses the novel challenges and opportunities of implementing an intervention that targets specific racial subgroup(s) in a community corrections setting that services all populations, implementing a group-based intervention with technological components in such settings, and employing community-based participatory research strategies to guide recruitment and retention efforts.Trial registrationClinicalTrials.gov, NCT02391233. Registered on 17 March 2015.Electronic supplementary materialThe online version of this article (10.1186/s13063-018-2792-3) contains supplementary material, which is available to authorized users.