Many HIV-infected injection drug users (IDUs) continue to use illicit substances despite being in substance use treatment. Substance use is associated with non-adherence to HIV medications; however underlying mechanisms regarding this relation are understudied. The current investigation examined the role of substance use coping in terms of the relation between substance use and HIV medication adherence. Participants were 121 HIV-infected IDUs (41 % female, M age = 47, SD = 7.1) in opioid dependence treatment. Participants completed self-report questionnaires, were administered clinical interviews and oral toxicology screens, and used a medication-event-monitoring-system cap to assess 2 week HIV medication adherence. The use of cocaine and multiple substances were significantly related to decreased medication adherence. Substance use coping mediated these associations. Findings highlight the importance of assessing, monitoring, and targeting ongoing substance use, and ways to increase positive coping for HIV-infected IDUs in substance use treatment to aid in HIV medication adherence.