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Introduction Food pantries are critical for addressing food insecurity, but dietary quality of food offered by pantries and selected by clients is often low. Supporting Wellness at Pantries (SWAP) is an evidence-based nutrition labelling strategy (eg, green=choose often; red=choose rarely) that has not been adopted widely due to implementation barriers. Behavioural economics (BE) strategies could help overcome these barriers.Methods and analysis The Be Well Study is testing a multicomponent BE intervention to increase implementation of SWAP in a 12-month cluster randomised controlled trial, followed by 12-month extended follow-up, in 30 pantries affiliated with a large food bank in eastern Massachusetts. During study months 1–12, intervention pantries receive the BE-enhanced SWAP implementation strategy including: SWAP toolkits, SWAP invoice labelling, dietitian-led learning communities, implementation incentives and the opportunity to earn a seal of approval. Control pantries receive basic SWAP information and invoice labelling. During extended follow-up (months 13–24), control pantries receive the BE intervention. Outcomes are assessed at the pantry (n=30) and client (n=3750) levels using pantry audits, food bank ordering data, client surveys and client basket audits and include changes from baseline to 6 and 12 (primary) months in: SWAP implementation, percent green-labelled foods ordered by pantries and selected by clients, and client dietary quality. During extended follow-up, these outcomes are assessed at 18 and 24 months. Be Well is testing strategies to overcome implementation barriers for healthy eating interventions in the charitable food system. Findings will inform future interventions to support pantry clients’ selection and consumption of healthier food.Ethics and dissemination Ethics approval was obtained from the institutional review board of Mass General Brigham (Protocols 2024P000832). Informed consent will be obtained from all participants. Findings will be disseminated through peer-reviewed journals, conferences and summaries shared with national and local stakeholders in the charitable food system.Trial registration number NCT06298253.