Background The COVID-19 pandemic has significantly disrupted primary care in Canada, with many walk-in clinics and family practices initially closing or being perceived as inaccessible; pharmacies remaining open with restrictions on patient interactions; rapid uptake of virtual care; and reduced referrals for lab tests, diagnostics, and specialist care. Objective The PUPPY Study (Problems in Coordinating and Accessing Primary Care for Attached and Unattached Patients Exacerbated During the COVID-19 Pandemic Year) seeks to understand the impact of the COVID-19 pandemic across the quadruple aims of primary care, with particular focus on the effects on patients without attachment to a regular provider and those with chronic health conditions. Methods The PUPPY study builds on an existing research program exploring patients’ access and attachment to a primary care practice, pivoted to adapt to the emerging COVID-19 context. We intend to undertake a longitudinal mixed methods study to understand critical gaps in primary care access and coordination, as well as compare prepandemic and postpandemic data across 3 Canadian provinces (Quebec, Ontario, and Nova Scotia). Multiple data sources will be used such as a policy review; qualitative interviews with primary care policymakers, providers (ie, family physicians, nurse practitioners, and pharmacists), and patients (N=120); and medication prescriptions and health care billing data. Results This study has received funding by the Canadian Institutes of Health Research COVID-19 Rapid Funding Opportunity Grant. Ethical approval to conduct this study was granted in Ontario (Queens Health Sciences & Affiliated Teaching Hospitals Research Ethics Board, file 6028052; Western University Health Sciences Research Ethics Board, project 116591; University of Toronto Health Sciences Research Ethics Board, protocol 40335) in November 2020, Québec (Centre intégré universitaire de santé et de services sociaux de l'Estrie, project 2020-3446) in December 2020, and Nova Scotia (Nova Scotia Health Research Ethics Board, file 1024979) in August 2020. Conclusions To our knowledge, this is the first study of its kind to explore the effects of the COVID-19 pandemic on primary care systems, with particular focus on the issues of patient’s attachment and access to primary care. Through a multistakeholder, cross-jurisdictional approach, the findings of the PUPPY study will inform the strengthening of primary care during and beyond the COVID-19 pandemic, as well as have implications for future policy and practice. International Registered Report Identifier (IRRID) DERR1-10.2196/29984