Background <p>Substance Use Disorder (SUD) is a chronic, relapsing condition that poses a significant public health challenge in Iraq. Evaluating the work system within specialized centers is essential for identifying barriers to effective patient management.</p> Objective <p>This study aimed to explore healthcare providers’ (HCPs) perspectives on factors shaping patient management and treatment acceptance in specialized SUD centers in Baghdad, utilizing the Systems Engineering Initiative for Patient Safety (SEIPS) model.</p> Method <p>A qualitative study was conducted between December 2023 and July 2024 at two specialized facilities: a social rehabilitation center (Site A) and an addiction treatment hospital (Site B). Semi-structured face-to-face interviews were held with 28 HCPs, including psychiatrists and nurses. Data were analyzed using Braun and Clarke’s thematic analysis framework and organized according to the five SEIPS domains: person, tasks, tools/technology, organization, and environment.</p> Results <p>Key findings across the SEIPS domains revealed significant systemic barriers. In the <i>Person domain</i>, HCPs highlighted inadequate specialized training and weak patient willpower fueled by the availability of substances. <i>Tasks</i> were characterized by the high effort required for continuous counseling and managing aggressive behavior. In <i>the Tools and Organization domains</i>, severe shortages of specialized staff, lack of electronic health records, and inadequate assessment spaces were reported. <i>Environmentally</i>, overcrowding and the “prison-like” atmosphere of facilities negatively impacted patient motivation.</p> Conclusion <p>Effective SUD management in Iraq is hindered by structural limitations, workforce shortages, and environmental stressors. Enhancing treatment outcomes requires a multidisciplinary approach, including specialized staff training, infrastructure modernization, and stronger inter-ministerial collaboration to address post-discharge relapse triggers.</p>