BackgroundThe charitable food system distributes free food to clients across the U.S., but many nutrition and health-focused efforts encounter barriers to success, which were exacerbated during the COVID-19 pandemic. The objective of the current study was to understand barriers and facilitators to distributing nutritious, fresh foods in food pantries across Illinois during the COVID-19 pandemic.MethodsForty-nine pantry representatives participated in focus groups in October 2021. A codebook was created based on relevant literature, stakeholder interests, and an initial review of the recordings. Transcripts of each group were coded and analyzed using a basic interpretive approach.ResultsPantries distribution of fresh foods was impacted by community partners, food bank policies and practices, and the quality of the donated fresh foods. Physical constraints of pantries limit fresh food storage capacity. The COVID-19 pandemic magnified stressors in the charitable food system which highlighted how community partners might improve fresh food distribution.ConclusionFocus groups with food pantry representatives across Illinois provided key insights that can inform future efforts to facilitate fresh food distribution in the charitable food system. Future studies should evaluate the effects of the suggested initiatives and changes at the food pantry, food bank, and policy levels.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-16215-4.