IntroductionContinuity of care, especially for patients with complex needs, is a major challenge for healthcare systems in many high-income countries, including Switzerland. Since 2015, a collaborative project between Unisanté-Department of Family Medicine (DMF), some general practitioners (GPs) and canton of Vaud’s public health authorities has sought to develop a new organisational model for the provision of primary care to ensure better care coordination and to provide adapted care deliveries to patients’ healthcare needs. The model’s main component is the addition of a primary care nurse to GPs practices. Three additional tools are individualised patient care plans, electronic medical records and patient empanelment. To assess this model, a 2-year pilot study has begun in nine GPs’ practices in the canton. This paper presents the protocol for an evaluation of the implementation and effectiveness of the new organisational model.Method and analysisWe will conduct a before-and-after study using a mixed-methods and a realist approach. First, we will use quantitative and qualitative data to assess the new organisational model’s implementation (feasibility, fidelity, acceptability and costs) and effectiveness (healthcare services use, patient experience, staff experience and patient-level costs). Combining this data with focus group data will enable a realist evaluation of the pilot project, which will help understand the elements of context and mechanism that affect implementation.Ethics and disseminationThe evaluation will inform the canton of Vaud’s health authorities about the limits of and perspectives for this organisational model. All results will also be made available to the practices and the patients involved. At the end of the project, we will propose organisational adaptations and a sustainable financial model for extending the model to other practices in the canton and potentially to the national level.The canton of Vaud’s Human Research Ethics Committee approved the study, and Data Protection and Information Law Authority gave a favourable opinion concerning data processing procedures.