Abstract Background Substance use disorders show a high comorbidity with externalizing behavior difficulties, creating treatment challenges, including difficulties with compliance, a high risk of conflict, and a high rate of offending post-treatment. Compared with people with other substance use disorders those with opioid use disorders have the highest risk of criminal activity, but studies on the evidence base for psychosocial treatment in opioid agonist treatment (OAT) are scarce. The Impulsive Lifestyle Counselling (ILC) program may be associated with better retention and outcomes among difficult-to-treat patients with this comorbidity. Methods The study is a multicenter, randomized, controlled, superiority clinical trial. Participants will be a total of 137 hard-to-treat individuals enrolled in opioid agonist treatment (OAT). Participants will be randomized to either a standard treatment (14 sessions of individual manual-based cognitive behavioral therapy and motivational interviewing (MOVE-I)) or six sessions of ILC followed by nine sessions of MOVE-I. All participants will receive personalized text reminders prior to each session and vouchers for attendance, as well as medication as needed. The primary outcome is retention in treatment. Secondary measures include severity of drug use and days of criminal offending for profit three and nine months post-randomization. A secondary aim is, through a case-control study, to investigate whether participants in the trial differ from patients receiving treatment as usual in municipalities where ILC and MOVE-I have not been implemented in OAT. This will be done by comparing number of offences leading to conviction 12 months post-randomization recorded in the national criminal justice register and number of emergency room contacts 12 months post-randomization recorded in the national hospital register. Discussion This is the first randomized, controlled clinical trial in OAT to test the effectiveness of ILC against a standardized comparison with structural elements to increase the likelihood of exposure to the elements of treatment. Results obtained from this study may have important clinical, social, and economic implications for publicly funded treatment of opioid use disorder. Trial registration ISRCTN, ISRCTN19554367 , registered on 04/09/2020.