BACKGROUND: Screening, Brief Intervention, and Referral to Treatment (SBIRT) is a clinical practice to identify and prevent risky health behaviors related to substance misuse. In preparation for SBIRT implementation assistance at a Federally Qualified Health Center (FQHC), Sedgwick County Health Department (SCHD) performed observational studies to identify current SBIRT-related workflow and inform recommendations for SBIRT implementation. METHODS: SCHD researched SBIRT processes and requirements. SCHD created an observational study form to document screening, substance use interventions, and referral and follow-up interactions of medical assistants, nurses, and medical and behavioral health providers. Study patients were age 18 or older and signed a confidentiality waiver prior to observations. RESULTS: In April 2019, SCHD observed 24 patient visits. Using observation data, SCHD created four SBIRT-related workflow process maps. Process maps revealed differences in perceived versus actual SBIRT-related clinic workflow. SCHD used process maps from observations and Kansas SBIRT requirements to draft a list of 20 SBIRT implementation recommendations. Recommendations included administering universal pre-screening questions verbatim and adding SBIRT processes to staff manuals. Challenges to completing the workflow observational studies included creating a workable process to secure authorization to observe patients, ensuring patients understood the purpose of study, and easing staff concerns related to being observed. CONCLUSION: Observational studies provided critical, objective data about current workflow processes and helped develop clinic-specific practices for SBIRT sustainability. The diverse expertise among SCHD, KUSM-W, and the clinic was essential to the success of the project.