Background: Rural, poor, persons with HIV (PWH) and substance use are among the most vulnerable to SARS-CoV-2 and related health service disruptions. The objective of the study was to evaluate the health outcomes and utilization of PWH at an Outpatient-based Opioid Treatment (OBOT) Clinic. Methods: We evaluated a clinic-based cohort at the University of Alabama at Birmingham HIV clinic from November 2018 to May 2021. We compared HIV outcomes of OBOT patients, who are highly vulnerable, to the overall clinic. We stratified OBOT patients according to comorbid stimulant use disorder and compared clinic utilization and viral load suppression in the 6 months before and after the safer at home mandate (May 2020) in Alabama. Results: Of 3857 PWH, 57 were referred to OBOT, 48 attended, 45 were initiated on buprenorphine, and 35 had a VL< 200 in the last 6 months. Relative to the overall HIV clinic, OBOT patients were significantly less likely to remain VL suppressed (90% vs 78%, p = 0.01). More patients were suppressed after OBOT linkage (81%) than prior (73%). For those referred before May 2020, there was no change in viral suppression before and after the safer at home order (75%). Although new OBOT referrals did not increase during the pandemic, the number of visits attended per month did increase from a median of 3–4 per patient. Conclusions: Unlike many PWH who faced access barriers, PWH receiving care at OBOT did not fall out of care but increased healthcare utilization and maintained viral suppression despite the public health emergency.