Background Given the close relationship that can exist between substance use health and mental health (SUHMH) concerns, the need for more integrated services and support has been identified. However, research on the effective integration of SUHMH services and their impact on outcomes of individuals accessing them remains limited. In particular, the unique outcomes of individuals facing significant structural inequities in the health care system, i.e., Indigenous Peoples in Canada, including First Nations, Inuit and Métis (FNIM), and equity-deserving (ED) groups, have not been evaluated while receiving integrated SUHMH services. This paper describes the protocol for a pilot research project, which will evaluate the change in clinical and social outcomes of individuals receiving integrated SUHMH services in relation to their intersectionality status, a linear score ranging from identifying with no FNIM and ED groups to identifying with one or multiple groups. Methods This study recruits 100 individuals who receive SUHMH services and support from a community health centre in Ottawa, Canada and assessed their FNIM and ED status and clinical and social outcomes at baseline and three-month follow-up. At the time of writing this manuscript, the baseline data collection was completed. Follow up assessment occurs three months after baseline data was collected. A smaller group of these participants will be purposefully selected match the proportion of FNIM and ED groups from the two-time assessment. They will be invited to participate in a post-data analysis validation consultation session to ensure that the findings are reflective of the experiences of individuals receiving SUHMH services, alternative interpretations are brought forward, and implications are driven by those who will be most impacted. This consultation may also inform knowledge mobilization activities and future studies. This study also recruited staff in different roles from the providing centre to rate the implementation of key dimensions of equity-oriented care into their practices and their level and capability to provide integrated services and support to individuals with cooccurring substance use disorders and mental illnesses. Discussion The results of this study will inform integrated SUHMH services by emphasizing equity and inclusive approaches, and engagement with the community.