BACKGROUND: Alcohol is one of the most important risk factors contributing to the global burden of disease. Screening and brief interventions in primary care settings are effective in reducing alcohol consumption. However, implementation of such interventions in routine practice has been proven difficult. Most programmes in practice and research have lacked a theoretical rationale for how they would change practitioner behaviour. OBJECTIVE: To determine whether a theory-based behaviour change intervention delivered to primary care practices significantly increases delivery of alcohol screening. METHODS: We will conduct a two-arm, cluster-randomized controlled, parallel, open trial. Twelve primary care practices will be randomized to one of two groups: training and support; and waiting-list control. Family physicians, nurses and receptionists will be eligible to participate. The intervention will be a training and support programme. The intervention will be tailored to the barriers and facilitators for implementing alcohol screening and brief interventions following the principles of the Behaviour Change Wheel approach. The primary outcome will be the proportion of patients screened with the Alcohol Use Disorders Identification Test. CONCLUSION: This study will test whether a theory-driven implementation programme increases alcohol screening rates in primary care. Results from this trial will provide a useful addition to existing evidence by informing implementation researchers what areas of behaviour change are critical to increasing alcohol screening rates. TRIAL REGISTRATION: clinicaltrials.gov NCT02968186.