Background The acute nature of the COVID-19 pandemic has put a strain on health resources that are usually dedicated to chronic illnesses. Resulting changes in care practices and networks have had major repercussions on the experience of people with chronic disorders. Objective This paper presents the protocol of the Parcours, Associations, Réseau, Chronicité, Organisation, Usagers, Retour d’expérience, Soins (PARCOURS)-COVID study. The aim of this study is to evaluate the effects of reorganization of the health system on the usual care network of patients with chronic illness, which fosters and qualifies the quality and continuum of care provided. The first objective of this study is to document these patients’ experiences through transformations and adaptations of their network, both in the practical dimension (ie, daily life and care) and subjective dimension (ie, psychosocial experience of illness and relationship to the health system). The second objective of the study is to understand and acknowledge these reorganizations during the COVID-19 lockdown and postlockdown periods. The third objective is to produce better adapted recommendations for patients with chronic illness and value their experience for the management of future health crisis. Methods The PARCOURS-COVID study is a qualitative and participatory research involving patient organizations as research partners and members of these organizations as part of the research team. Three group of chronic diseases have been selected regarding the specificities of the care network they mobilize: (1) cystic fibrosis and kidney disease, (2) hemophilia, and (3) mental health disorders. Four consecutive phases will be conducted, including (1) preparatory interviews with medical or associative actors of each pathology field; (2) in-depth individual interviews with patients of each pathology, analyzed using the qualitative method of thematic analysis; (3) results of both these phases will then be triangulated through interviews with members of each patient’s care ecosystem; and finally, (4) focus groups will be organized to discuss the results with research participants (ie, representatives of chronic disease associations; patients; and actors of the medical, psychosocial, and family care network) in a research-action framework. Results The protocol study has undergone a peer review by the French National Research Agency’s scientific committee and has been approved by the research ethical committee of the University of Paris (registration number: IRB 00012020-59, June 28, 2020). The project received funding from August 2020 through April 2021. Expected results will be disseminated in 2021 and 2022. Conclusions Our findings will better inform the stakes of the current health crisis on the management of patients with chronic illness and, more broadly, any future crisis for a population deemed to be at risk. They will also improve health democracy by supporting better transferability of knowledge between the scientific and citizen communities. International Registered Report Identifier (IRRID) DERR1-10.2196/28728