Given the interrelated nature of opioid use, criminal justice interaction, and mental health issues, the current opioid crisis has created an urgent need for treatment, including medication assisted treatment, among justice-involved populations. Implementation research plays an important role in improving systems of care and integration of evidence-based practices within and outside of criminal justice institutions. The current study is a formative qualitative evaluation of the implementation of a cross-system (corrections and community-based) opioid use treatment initiative supported by Opioid State Targeted Response (STR) funding. The purpose of the study is to assess the fit of the Consolidated Framework for Implementation Research (CFIR) to a cross-system initiative, and to identify key barriers and facilitators to implementation. The process evaluation showed that adaptability of the clinical model and staff flexibility were critical to implementation. Cultural and procedural differences across correctional facilities and community-based treatment programs required frequent and structured forums for cross-system communication. Challenges related to recruitment and enrollment, staffing, MAT, and data collection were addressed through the collaborative development and continuous review of policies and procedures. This study found CFIR to be a useful framework for understanding implementation uptake and barriers. The framework was particularly valuable in reinforcing the use of implementation research as a means for continuous process improvement. CFIR is a comprehensive and flexible framework that may be adopted in future cross-system evaluations.