Alcohol use disorders (AUD) in individuals with mental illness are largely untreated. The purpose of this study was to identify gaps in organizational capacity and readiness to provide medications for AUD in outpatient public mental health clinics. We selected a purposive sample of eight publicly funded outpatient mental health clinics operated by the Los Angeles County Department of Mental Health; clinics were chosen to maximize heterogeneity. Guided by theories of organizational capacity and readiness and research on the adoption of pharmacotherapy for AUD in primary and specialty care treatment settings, we conducted semi-structured interviews and focus groups with administrators, providers and staff, and a qualitative analysis of the results. Respondents described significant organizational capacity and behavioral readiness constraints to providing medication treatment for AUD. Both groups articulated a perception that mental health clinics were not designed to provide co-occurring AUD treatment because of large caseloads, staffing configurations, and time constraints that did not support the delivery of appropriate treatment, and a lack of protocols and workflow procedures. We documented organizational capacity and readiness constraints which impede the delivery of medication treatment for AUD in a large mental health system. While some constraints have straightforward solutions, others require structural changes to the way care is delivered, and state-level funding and policy changes.