The Brazilian National School Feeding Programme aims to ensure food security and the right to food for public school students. To protect these fundamental rights, a comprehensive approach is needed that includes ensuring food safety. Recognising that low socio-economic conditions, inadequate food safety and child vulnerability can pose a cumulative burden on child development, this study examined food safety in public schools in Sergipe, Brazil, in the context of local socio-economic indicators. All state public schools in Sergipe (n = 314) were included. Food safety and socio-economic data were analysed using secondary sources and geographical maps. The cluster analysis identified two different groups of schools based on socio-economic indicators. While most schools presented regular foodborne illness risks, food production and temperature control had particularly high levels of non-compliance. Schools in areas with higher socio-economic indicators (Cluster 2) had better overall food safety scores (p < 0.001) compared to schools in areas with lower socio-economic indicators (Cluster 1). Cluster 1 schools also had a higher FBI risk when analysing temperature-controlled equipment violations (p = 0.001), food handlers (p = 0.005) and process and production (p = 0.004), which emerged as critical areas. These results emphasise the urgent need for targeted interventions to improve food safety in schools located in areas with lower socio-economic conditions.