Primary care is an opportune setting to deliver treatments for co-occurring substance use and mental health disorders; however, treatment delivery can be challenging due multi-level implementation barriers. Documenting organizational context can provide insight into implementation barriers and the adaptation of new processes into usual care workflows. This study surveyed primary care and behavioral health staff from 13 clinics implementing a collaborative care intervention for opioid use disorders co-occurring with PTSD and/or depression as part of a multisite randomized controlled trial. A total of 323 completed an online survey for a 60% response rate. The Consolidated Framework for Implementation Research guided this assessment of multi-level factors that influence implementation. Most areas for improvement focused on inner setting (organizational level) constructs whereas individual-level constructs tended to be strengths. This work addresses a research gap regarding how organizational analyses can be used prior to implementation and provides practical implications for researchers and clinic leaders.