Evidence-based approaches to screening and treatment for unhealthy alcohol use have the potential to reduce morbidity and mortality but are currently underutilized in primary care settings. To support implementation of screening, brief intervention, and referral to treatment (SBIRT) and medication-assisted treatment for alcohol use disorder (MAUD) by identifying goals co-developed by clinics and practice facilitators in a flexible implementation study. In a pragmatic implementation study, we used practice facilitation to support the implementation of SBIRT and MAUD in 48 clinical practices across Oregon, Washington, and Idaho. Our study used a tailored approach, in which facilitators and clinics co-identified implementation goals based on clinic needs. We used clinic contact logs, individual interviews, group periodic reflections with practice facilitators, and exit interviews with clinic staff to inform qualitative analysis. With support from practice facilitators, clinics identified goals spanning SBIRT, MAUD, reporting, targeted patient outreach, and quality improvement capacity. Goals addressed both the technical (e.g. data tracking) and social (e.g. staff training) aspects of SBIRT and MAUD. A decision tree summarizes emergent findings into a tool to support future implementation of SBIRT in primary care settings. A facilitator-supported, tailored approach to SBIRT implementation enabled clinics to identify a variety of goals to improve SBIRT and MAUD implementation. These identified priorities, along with a decision tree describing the hierarchical structure of these goals, could support future implementation efforts.