BACKGROUND: Unhealthy alcohol use is an unaddressed barrier to achieving and maintaining control of the human immunodeficiency virus (HIV) epidemic. Integrated screening, treatment of common behavioral and mental health comorbidities, and telemedicine can improve alcohol treatment and HIV clinical and quality of life outcomes for rural and underserved populations. OBJECTIVE: In a randomized controlled clinical trial, we will evaluate the effectiveness and implementation of telephone-delivered Common Elements Treatment Approach (T-CETA), a transdiagnostic cognitive behavioral therapy protocol, on unhealthy alcohol use, HIV, other substance use and mental health outcomes among predominantly rural adults with HIV receiving care at community clinics in Alabama. METHODS: Adults with HIV receiving care at four selected community clinics in Alabama will receive a telephone-delivered alcohol brief intervention (BI), and then be assigned at random (stratified by clinic and sex) to no further intervention or T-CETA. Participants will be recruited after screening positively for unhealthy alcohol use or when referred by a provider. The target sample size is 308. The primary outcome will be change in the Alcohol Use Disorder Identification Test (AUDIT) at six- and 12-months post-enrollment. Additional outcomes include HIV (retention in care and viral suppression), patient-reported mental health (anxiety, depression, posttraumatic stress), and quality of life. A range of implementation measures be evaluated including T-CETA provider and client acceptability, feasibility, cost and cost-effectiveness. CONCLUSIONS: This trial will inform alcohol treatment within HIV care programs, including the need to consider comorbidities, and the potential impact of alcohol interventions on HIV and quality of life outcomes.