IntroductionHazardous alcohol and drug use is associated with substantial morbidity, mortality and societal cost worldwide. Yet, only a minority of those struggling with substance use concerns receive specialised services. Numerous barriers to care exist, highlighting the need for scalable and engaging treatment alternatives. Online interventions have exhibited promise in the reduction of substance use, although studies to date highlight the key importance of patient engagement to optimise clinical outcomes. Peer support may provide a way to engage patients using online interventions. The goal of this study is to evaluate the efficacy and cost-effectiveness of Breaking Free Online (BFO), an online cognitive-behavioural intervention for substance use, delivered with and without peer support.Methods and analysisA total of 225 outpatients receiving standard care will be randomised to receive clinical monitoring with group peer support, with BFO alone, or with BFO with individual peer support, in an 8-week trial with a 6-month follow-up. The primary outcome is substance use frequency; secondary outcomes include substance use problems, depression, anxiety, quality of life, treatment engagement and cost-effectiveness. Mixed effects models will be used to test hypotheses, and thematic analysis of qualitative data will be undertaken.Ethics and disseminationThe protocol has received approval by the Centre for Addiction and Mental Health Research Ethics Board. Results will help to optimise the effectiveness of structured online substance use interventions provided as an adjunct to standard care in hospital-based treatment programmes. Findings will be disseminated through presentations and publications to scholarly and knowledge user audiences.Trial registration numberNCT05127733