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Abstract Background Moral Reconation Therapy (MRT) is a cognitive-behavioral intervention aimed at reducing risk for criminal recidivism by restructuring antisocial attitudes and cognitions (i.e., “criminogenic thinking”). MRT has empirical support for reducing risk for criminal recidivism among civilian offenders. Recently, a version of MRT was developed for military veterans; however, no randomized controlled trials (RCT) have been conducted with the veteran-specific protocol, and the effectiveness and implementation potential of MRT outside of correctional settings has not been established. Methods Using a Hybrid Type 1 RCT design, this study will test the effectiveness of MRT to reduce risk for criminal recidivism and improve health-related outcomes among justice-involved veterans entering mental health residential treatment at three US Veterans Health Administration (VHA) Medical Centers. Upon admission to the treatment program, justice-involved veterans will complete a baseline assessment, be randomized to usual care (UC) or UC + MRT, and be followed 6 and 12 months post-baseline. A process evaluation will also be conducted to identify barriers and facilitators to implementation of MRT in residential treatment. Discussion The primary aim of this study is to evaluate the effectiveness of MRT with justice-involved veterans. If MRT proves effective in this trial, the findings can provide large healthcare systems that serve veterans with an evidence-based intervention for addressing criminogenic thinking among justice-involved adults, as well as guidance on how to facilitate future implementation of MRT in non-correctional settings. Trial registration This trial is funded by the VA Health Services Research & Development Program (IIR 14–081) and is registered with ClinicalTrials.gov (ID: NCT02524171).