Background Undernutrition threatens the health and future of preschool children in disadvantaged ethnic minority communities. Home-grown school feeding (HGSF) in nursery schools could have a positive impact on children’s nutrition while creating multiple benefits for the community and local food system. Evidence is lacking on the implementation and sustainability of HGSF as part of multi-sectoral programs in remote areas. This study assessed a HGSF pilot intervention, implemented within a four-year nutrition-sensitive agriculture (NSA) program, in five nursery schools in a mountain ethnic minority community in Vietnam. It aimed to gain insights into the diversity and cost of school meals, food sources, effects on children’s nutritional status and on process aspects related to implementation and sustainability, especially HGSF synergy with other NSA program components. Methods Mixed-methods assessment covered school meal diversity and cost; food sources; anthropometric data; and the process, including changes triggered by HGSF, perceived barriers and facilitators to implementation, and prospects for sustainability. Data came from participants selected by purposive sampling for semi-structured interviews (n = 30) and seven focus group discussions (n = 76), and from field observations and transect walks. Results School meals increased daily dietary diversity; meals cost USD 0.65/child/day. About 44% of the foods used were home-grown. There was an indicative reduction in underweight children, an increase in school attendance, and improvements in food preferences and WASH practices. Parents’ caring and feeding practices improved and their willingness to pay for school meals increased. At community level, local food systems became less cash crop-oriented and more self-reliant in production of nutrient-rich foods, contributing to household food security and income generation. Social capital increased. Positive changes were attributed to HGSF and to synergy among NSA program components. Enhanced confidence and motivation, stimulated by role models and change agents, facilitated the process. Socio-economic conditions of poor households and limited resilience to external shocks were barriers that threatened sustainability. Conclusions This study showed that implementing HGSF in a mountain ethnic minority area with a high prevalence of undernutrition benefitted children and their communities, when integrated in a multi-sectoral program that mobilises all stakeholders and stimulates both supply and demand of nutritious food.