Background: Antiretroviral stock-outs in conflict-affected regions like Libya disrupt essential HIV treatment, risking viral suppression and health outcomes. However, the specific clinical impact of these interruptions remains critically under-researched. Methods: A mixed-methods study at Tripoli Central Hospital included a review of 230 HIV patient records and questionnaires from 16 healthcare workers. The retrospective analysis examined ART outcomes like viral load suppression and CD4 changes (per WHO/UNAIDS guidelines), using multivariable regression to find factors linked to poor results. The cross-sectional part assessed staff experiences with ARV stock-outs. Results: The study of 230 participants (96.5% living with HIV) provides a comprehensive analysis of the clinical impact of antiretroviral (ARV) stock-outs in Libya. The cohort was predominantly male (66.1%) with a mean age of 42.3 years. Among 219 patients on chronic ART, 51.1% experienced regimen modifications, with 85% of these shifts necessitated by drug unavailability. The clinical outcomes for those on stable regimens were significantly superior, achieving 75% viral suppression and higher mean CD4 counts (450 cells/µL) compared to 45% suppression and 250 cells/µL in patients with multiple regimen changes (p < 0.01). Notably, 92% of patients experiencing disruptions remained engaged in care. Additionally, the study confirmed the efficacy of sofosbuvir/daclatasvir for HIV/HCV co-infections and the success of prophylactic protocols in preventing new HIV transmissions. Conclusion: ARV stock-outs and forced regimen substitutions are associated with adverse HIV treatment outcomes in Libya. Strengthening ARV supply chain resilience, expanding clinical pharmacy services, and integrating digital health systems are critical to improving treatment continuity and optimizing patient outcomes in conflict-affected settings.