Background: Over 1100 Veterans work in the Veterans Health Administration (VHA) as peer specialists (PSs). PSs are Veterans with formal training who provide support to other Veterans with similar diagnoses, primarily in mental health settings. A White House Executive Action mandated the pilot reassignment of VHA PSs from mental health to 25 primary care Patient Aligned Care Teams (PACT) in order to broaden the provision of wellness services that can address many chronic illnesses. An evaluation of this initiative was undertaken to assess the impact of outside assistance on the deployment of PS in PACT, as implementation support is often needed to prevent challenges commonly experienced when first deploying PSs in VHA settings. We present the protocol for this cluster-randomized hybrid type II trial to test the impact of standard implementation (receive minimal assistance) vs. facilitated implementation (receive outside assistance) on the deployment of VHA PSs in PACT. Methods: A VHA Office of Mental Health Services work group is recruiting 25 Veterans Affairs Medical Centers to reassign a mental health PSs to provide wellness-oriented care in PACT. Sites in three successive cohorts (n = 8, 8, 9) beginning over 6-month blocks will be matched and randomized to either standard or facilitated implementation. In facilitated implementation, an outside expert works with site stakeholders through a site visit, regular calls, and performance data to guide the planning and address challenges. Standard implementation sites will receive a webinar and access the Office of Mental Health Services work group. The two conditions will be compared on PS workload data, fidelity to the PS model of service delivery, team functioning, and Veteran measures of activation, satisfaction, and functioning. Qualitative interviews will collect information on implementation barriers and facilitators. Discussion: This evaluation will provide critical data to guide administrators and VHA policy makers on future deployment of PSs, as their role has been expanding beyond mental health. In addition, development of novel implementation strategies (facilitation tailored to PSs) and the use of new tools (peer fidelity) can be models for monitoring and supporting deployment of PSs throughout VHA.