BACKGROUND: Approximately one-third of all patients with schizophrenia are treatment resistant. Worldwide, undertreatment with clozapine and other effective treatment options exist for people with treatment-resistant schizophrenia (TRS). In this respect, it appears that regular health care models do not optimally fit this patient group. The Collaborative Care (CC) model has proven to be effective for patients with severe mental illness, both in primary care and in specialized mental health care facilities. The key principles of the CC model are that both patients and informal caregivers are part of the treatment team, that a structured treatment plan is put in place with planned evaluations by the team, and that the treatment approach is multidisciplinary in nature and uses evidence-based interventions. We developed a tailored CC program for patients with TRS. OBJECTIVE: In this paper, we provide an overview of the research design for a potential study that seeks to gain insight into both the process of implementation and the preliminary effects of the CC program for patients with TRS. Moreover, we aim to gain insight into the experiences of professionals, patients, and informal caregivers with the program. METHODS: This study will be underpinned by a multiple case study design (N=20) that uses a mixed methods approach. These case studies will focus on an Early Psychosis Intervention Team and 2 Flexible Assertive Community treatment teams in the Netherlands. Data will be collected from patient records as well as through questionnaires, individual interviews, and focus groups. Patient recruitment commenced from October 2020. RESULTS: Recruitment of participants commenced from October 2020, with the aim of enrolling 20 patients over 2 years. Data collection will be completed by the end of 2023, and the results will be published once all data are available for reporting. CONCLUSIONS: The research design, framed within the process of developing and testing innovative interventions, is discussed in line with the aims of the study. The limitations in clinical practice and specific consequences of this study are explained. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/35336.