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Introduction In 2011, the Canadian Institutes of Health Research launched a Strategy for Patient-Oriented Research (POR) for healthcare and academic institutions to increase patient participation in health research. POR considers patients and caregivers as partners with scientific investigators, healthcare professionals and administrative decision-makers. As POR becomes a standard worldwide, the how-to, practical aspects of POR integration in healthcare institutions remain uncharted territory. A more accurate POR range in health research would improve healthcare systems. Yet the availability of standardised accreditation has not been achieved. The research question for this scoping review arose from a patient-partner in our team who experienced organisational challenges in healthcare institutions related to her role. It will overview and map the available evidence of organisational structures and changes that enable the integration of POR within healthcare institutions globally. This should serve our future projects to propose standardised pan-Canadian POR accreditation protocols.Methods and analysis Following Joanna Briggs Institute (JBI) methods and predetermined eligibility, we will perform a qualitative scoping review, searching for healthcare institution’s organisational structures and changes in Patient-Oriented Research (POR)-related accreditation, criteria and procedures in academic peer-reviewed databases and grey literature. The scoping review’s steps are as follows: (1) framing the research question; (2) targeting the documentation; (3) selecting documents by two reviewers; (4) charting/extracting data; (5) summarising and reporting the results. The search strategy will be applied to three databases for academic literature, and a search for grey literature will be performed. Emergent documents from academic studies or grey literature describing the organisational structure or changes to integrate POR within healthcare institutions, from 2012 to the present and in English or French, will be included. All articles will be analysed by two reviewers individually for inclusion. Extracted quantitative and qualitative data will describe eligible studies and POR-relevant elements. Tables mapping the organisational structures will be presented.Ethics and dissemination The methodology consists of exploring published evidence; therefore, ethics approval is not required. Patient-partners will provide feedback on findings and strategies for disseminating the results. Dissemination activities will include peer-reviewed publication, co-creation of teaching seminars and academic presentations.Trial registration number The review was registered prospectively with Open Science Framework (OSF). Available: https://osf.io/4t6ud.