Background Identifying and treating problem alcohol use among people who also use illicit drugs is a challenge. Primary care is well placed to address this challenge but there are several barriers which may prevent this occurring. The objective of this study was to determine if a complex intervention designed to support screening and brief intervention for problem alcohol use among people receiving opioid agonist treatment is feasible and acceptable to healthcare providers and their patients in a primary care setting. Methods A randomised, controlled, pre-and-post design measured feasibility and acceptability of alcohol screening based on recruitment and retention rates among patients and practices. Efficacy was measured by screening and brief intervention rates and the proportion of patients with problem alcohol use. Results Of 149 practices that were invited, 19 (12.8 %) agreed to participate. At follow up, 13 (81.3 %) practices with 81 (62.8 %) patients were retained. Alcohol screening rates in the intervention group were higher at follow up than in the control group (53 % versus 26 %) as were brief intervention rates (47 % versus 19 %). Four (18 %) people reduced their problem drinking (measured by AUDIT-C), compared to two (7 %) in the control group. Conclusions Alcohol screening among people receiving opioid agonist treatment in primary care seems feasible. A definitive trial is needed. Such a trial would require over sampling and greater support for participating practices to allow for challenges in recruitment of patients and practices. Electronic supplementary material The online version of this article (doi:10.1186/s12875-016-0548-2) contains supplementary material, which is available to authorized users.