Diarrhoeal disease in children under five in low income settings has been associated with multiple environmental exposure pathways, including complementary foods. Conducted from February to December 2018 in rural Malawi, this before and after trial with a control used diarrhoeal disease as a primary outcome, to measure the impact of a food hygiene intervention (food hygiene + handwashing) relative to a food hygiene and water, sanitation and hygiene (WASH) intervention (food hygiene + handwashing + faeces management + water management). The 31-week intervention was delivered by community-based coordinators through community events (n = 2), cluster group meetings (n = 17) and household visits (n = 14). Diarrhoeal disease was self-reported and measured through an end line survey, and daily diaries completed by caregivers. Difference-in-differences results show a 13-percentage point reduction in self-reported diarrhoea compared to the control group. There were also significant increases in the presence of proxy measures in each of the treatment groups (e.g., the presence of soap). We conclude that food hygiene interventions (including hand washing with soap) can significantly reduce diarrhoeal disease prevalence in children under five years in a low-income setting. Therefore, the promotion of food hygiene practices using a behaviour-centred approach should be embedded in nutrition and WASH policies and programming.