This paper describes the process we undertook to implement Screening, Brief Intervention, and Referral to Treatment (SBIRT) and the Workplace Outcome Suite (WOS) as part of a larger continuous quality improvement initiative in an internal employee assistance program (EAP). Located in the Boston area, Partners EAP is an accredited internal EAP that is a voluntary service available to over 74,000 employees of Partners HealthCare System and their immediate household members. The authors examine the process improvement strategies enacted to conduct routine screenings for alcohol, drugs, and depression, and pre and post measurement of five outcomes designed for EAPs. This paper also explores how the EAP changed the operational practices and procedures to implement these behavioral health screening tools and measures. Lessons learned and recommendations are offered to facilitate and overcome barriers to integrating screening tools and collecting outcomes data.