Banana and plantain are one of the most important staple food crops and a significant source of income to smallholder farmers in the East African Great Lakes Region. Banana Xanthomonas Wilt (BXW) is a devastating bacterial disease that threatens smallholder production and livelihoods. We use a systems approach to describe how gender shapes roles and practices in the household, on the farm and in innovation processes. We draw on a case study in Burundi, where single disease stem removal (SDSR) has been introduced as a labour-saving package to reduce BXW incidence.