Background Living Labs are user-centered, open innovation ecosystems based on a systematic user cocreation approach, which integrates research and innovation processes in real-life communities and settings. The Horizon 2020 Project VITALISE (Virtual Health and Wellbeing Living Lab Infrastructure) unites 19 partners across 11 countries. The project aims to harmonize Living Lab procedures and enable effective and convenient transnational and virtual access to key European health and well-being research infrastructures, which are governed by Living Labs. The VITALISE consortium will conduct joint research activities in the fields included in the care pathway of patients: rehabilitation, transitional care, and everyday living environments for older adults. This protocol focuses on health and well-being research in everyday living environments. Objective The main aim of this study is to cocreate and test a harmonized research protocol for developing big data–driven hybrid persona, which are hypothetical user archetypes created to represent a user community. In addition, the use and applicability of innovative technologies will be investigated in the context of various everyday living and Living Lab environments. Methods In phase 1, surveys and structured interviews will be used to identify the most suitable Living Lab methods, tools, and instruments for health-related research among VITALISE project Living Labs (N=10). A series of web-based cocreation workshops and iterative cowriting processes will be applied to define the initial protocols. In phase 2, five small-scale case studies will be conducted to test the cocreated research protocols in various real-life everyday living settings and Living Lab infrastructures. In phase 3, a cross-case analysis grounded on semistructured interviews will be conducted to identify the challenges and benefits of using the proposed research protocols. Furthermore, a series of cocreation workshops and the consensus seeking Delphi study process will be conducted in parallel to cocreate and validate the acceptance of the defined harmonized research protocols among wider Living Lab communities. Results As of September 30, 2021, project deliverables Ethics and safety manual and Living lab standard version 1 have been submitted to the European Commission review process. The study will be finished by March 2024. Conclusions The outcome of this research will lead to harmonized procedures and protocols in the context of big data–driven hybrid persona development among health and well-being Living Labs in Europe and beyond. Harmonized protocols enable Living Labs to exploit similar research protocols, devices, hardware, and software for interventions and complex data collection purposes. Economies of scale and improved use of resources will speed up and improve research quality and offer novel possibilities for open data sharing, multidisciplinary research, and comparative studies beyond current practices. Case studies will also provide novel insights for implementing innovative technologies in the context of everyday Living Lab research. International Registered Report Identifier (IRRID) DERR1-10.2196/34567