BACKGROUND: Coordinated Specialty Care (CSC) programs provide evidence-based services for young people with a recent onset of a psychotic disorder. OnTrackNY is a nationally recognized model of CSC treatment in New York state. In 2019, OnTrackNY was awarded a hub within the Early Psychosis Intervention Network (EPINET) to advance its learning health care system (LHS). The OnTrackNY network is comprised of 23 CSC teams across New York state. OnTrack Central, an intermediary organization, provides training and implementation support to OnTrackNY teams. OnTrack Central coordinates a centralized data collection protocol for quality improvement and evaluation of program fidelity and a mechanism to support practice based-research. OnTrackNY sites' breadth coupled with OnTrack Central oversight provides an opportunity to examine the impacts of the COVID-19 crisis in New York State, and supplementary funding was awarded to the OnTrackNY EPINET hub in 2021 for that purpose. METHODS: This project will examine the implications of modifications to service delivery within the OnTrackNY LHS during and after the COVID-19 crisis. We will use the Framework for Reporting Adaptations and Modification-Enhanced (FRAME) to classify systematically, code, and analyze modifications to CSC services and ascertain their impact. We will utilize integrative mixed methods. Qualitative interviews with multi-level stakeholders (program participants, families, providers, team leaders, agency leaders, trainers (OnTrack Central), and decision-makers at the state and local levels) will be used to understand the process of making decisions, information about modifications to CSC services, and their impact. Analysis of OnTrackNY program data will facilitate examining trends in team staffing and functioning, and participant service utilization and outcomes. Study findings will be summarized in a CSC Model Adaptation Guide, which will identify modifications as fidelity consistent or not, and their impact on service utilization and care outcomes. DISCUSSION: A CSC Model Adaptation Guide will inform CSC programs, and the state and local mental health authorities to which they are accountable, regarding modifications to CSC services and the impact of these changes on care process, and participant service utilization and outcomes. The guide will also inform the development of tailored technical assistance that CSC programs may need within OnTrackNY, the EPINET network, and CSC programs nationally. TRIAL REGISTRATION: NCT04021719 , July 16th, 2019.