Background: The co-occurrence of domestic violence with alcohol and other drugs significantly increases the severity of abuse and violence experienced by family members. Longitudinal studies indicate that substance use is one of few predictors of men’s continued use of, or desistance from, violence. Recent developments in men’s behaviour change programs have focused on men’s attitudes and behaviour towards their children, and the exploration of interventions that address the needs of all family members. However, the research evidence is limited on the most effective elements of men’s behaviour change programs in promoting the safety and wellbeing of child and women victim survivors. This study aims to build on the existing evidence by trialling the KODY program which addresses harmful substance use by men who also perpetrate domestic violence; the safety and wellbeing of women and children; the needs of children in their own right, as well as in relationship with their mothers; and the development of an ‘all-of-family’ service response. The evaluation of these innovations, and the ramifications for policy development to support less fragmented service system responses, provide the rationale for the study. Methods/Design: A quasi-experimental design will be used to assess the primary outcomes of improving the safety and wellbeing of mothers and children whose (ex)partners and fathers respectively participate in KODY (the trial program), when compared with ‘Caring Dads standard’ (the comparison group). Psychometric tests will be administered to fathers and mothers at baseline, post-program and at 3-month follow up. Data collection will occur over three years. Discussion: By building the evidence base about responses to co-occurring domestic violence and substance use, this study aims to develop knowledge about improving safety outcomes for women and children, and to better understand appropriate support for children in families living at the intersection of domestic violence and substance use. It is anticipated that study findings will point to the ramifications for policy development to support less fragmented service system responses. Trial registration: An application for registration with the Australian and New Zealand Clinical Trials Registry (https://www.anzctr.org.au/) was lodged on 20 December 2021 (Request number: 383206)—prospectively registered.