School nutrition programs mitigate food insecurity and promote healthy eating by offering consistent, nutritious meals to school-aged children in communities across the United States; however, stringent policy guidelines and contextual challenges often limit participation. During COVID-19 school closures, most school nutrition programs remained operational, adapting quickly and innovating to maximize reach. This study describes semi-structured interviews with 23 nutrition directors in North Carolina, which aimed to identify multi-level contextual factors that influenced implementation, as well as ways in which the innovations during COVID-19 could translate to permanent policy and practice change and improve program reach. Interviews were conducted during initial school closures (May–August 2020) and were deductively analyzed using the Social Ecological Model (SEM) and Consolidated Framework for Implementation Research (CFIR). Analysis elicited multiple relevant contextual factors: director characteristics (motivation, leadership style, experience), key implementation stakeholders (internal staff and external partners), inner setting (implementation climate, local leadership engagement, available resources, structural characteristics), and outer setting (state leadership engagement, external policies and incentives). Findings confirm the strength and resilience of program directors and staff, the importance of developing strategies to strengthen external partnerships and emergency preparedness, and strong support from directors for policies offering free meals to all children.