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Background: Local food environments are recognized by experts as a determinant of healthy eating. Food cooperatives (coop) can promote the accessibility to healthier foods and thus improve the health of the population, particularly in remote rural communities. Objective: To measure the effects of implementing a food coop in a disadvantaged community with poor access to food. We have two main research questions: (1). Does the establishment of a food coop in rural areas described as food deserts have an impact on accessibility, frequency of use, food consumption, food quality, and ultimately the health of individuals? (2). Does the establishment of a food coop in rural areas described as food deserts have an impact on food security and community vitality? Design: A natural experiment with a mixed pre/post method will be used. The sample is composed of households that came from geographically isolated communities (population: 215 to 885 inhabitants) which qualified as food deserts and located in rural areas of Quebec (Canada). All communities plan to open a food coop (in the years 2022–2023), and as their opening will be staggered over time, participants from communities with a new food coop (intervention) will be compared to communities awaiting the opening of their food coop (control). Data collection was carried out at three time points: (1) before; (2) 1 to 5 months after; and (3) 13 to 17 months after the opening of the coop. Questionnaires were used to measure sociodemographic variables, dietary intake, residents’ health, and community vitality. Semi-structured interviews were conducted with community stakeholders. Results: Few natural experiments have been conducted regarding the impact of implementing food coops. Gathering concrete data on the effectiveness and processes surrounding these interventions through natural experiments will help to quantify their impact and guide knowledge users and policymakers to make more informed decisions.