In Australia, school canteens are an integral part of the school environment and an ideal site to encourage healthy eating. However, when the canteen is not supported within the school system, healthy menus may be difficult to implement. The aim of this study was to investigate school canteens and their place within the school system in primary and secondary schools in South Australia. Using a systems approach, 14 schools and their canteens located throughout metropolitan and rural South Australia are discussed. A range of qualitative interviews was conducted with school principals (n = 14), canteen managers (n = 14), parents (n = 50), teachers (n = 10) and focus group interviews were held with students (n = 450). This study showed that although school canteens were located on school grounds and should be supported as an integral part of the school system, in many cases they were not. A range of influences such as: maintaining profit, reduced volunteer support and student choice negatively impacted what was sold on the canteen menu. This study indicated that offering a sustainable healthy school canteen menu largely depended on the support and resources provided to the canteen by the school system in which it belonged.