BACKGROUND: Contemporary studies about HIV care continuum (HCC) outcomes within substance using populations primarily focus on individual risk factors rather than provider- or systems-level influences. Over 25% of people living with HIV (PLWH) have substance use disorders that can alter their path through the HCC. As part of a study of HCC outcomes in nine small cities in Southern New England (population 100,000-200,000 and relatively high HIV prevalence particularly among substance users), this qualitative analysis sought to understand public health staff and HIV service providers' perspectives on how substance use may influence HCC outcomes. METHODS: Interviews with 49 participants, collected between November 2015 and June 2016, were analyzed thematically using a modified social ecological model as the conceptual framework and codes for substance use, HCC barriers and facilitators, successes and failures of initiatives targeting the HCC, and criminal justice issues. RESULTS: Eight themes were identified concerning the impact of substance use on HCC outcomes. At the individual level, these included coping and satisfying basic needs and could influence all HCC steps (i.e., testing, treatment linkage, adherence, and retention, and viral load suppression). The interpersonal level themes included stigma issues and providers' cultural competence and treatment attitudes and primarily influenced treatment linkage, retention, and viral load suppression. These same HCC steps were influenced at the health care systems level by organizations' physical environment and resources as well as intra-/inter-agency communication. Testing and retention were the most likely steps to affect at the policy/society level, and the themes included opposition within an organization or community, and activities with unintended consequences. CONCLUSIONS: The most substantial HCC challenges for PLWH with substance use problems included linking and retaining in treatment those with multiple co-morbidities and meeting their basic living needs. Recommendations to improve HCC outcomes for PLWH with substance use problems include increasing easy access to effective drug and mental health treatment, expanding case management and peer navigation services, training staff about harm reduction, de-stigmatizing, and culturally competent approaches to interacting with patients, and increasing information-sharing and service coordination among service providers and the social service and criminal justice systems.