Diarrhoeal disease remains one of the leading causes of morbidity and mortality in the under-five population, particularly in low income settings such as sub-Saharan Africa. Despite significant progress in sanitation and water access, faecal-oral infections persist in these populations. Therefore, a better understanding of these transmission pathways, and how potential risk factors can be reduced within low income contexts is needed. This study, conducted in Southern Malawi from June to October 2017, used a mixed methods approach to collect data from household surveys (n = 323), checklists (n = 31), structured observations (n = 80), and microbiological food samples (n = 20). Results showed that food prepared for immediate consumption (primarily porridge for children) posed a low health risk. Poor hygiene practices increased the risk of contamination from shared family meals. Faecal and nosocomial bacteria were associated with poor hand hygiene and unhygienic eating conditions. Leftover food storage and inadequate pre-consumption heating increased the risk of contamination. Improvements in food hygiene and hand hygiene practices at critical points could reduce the risk of diarrhoeal disease for children under 2 years but must consider the contextual structural barriers to improved practice like access to handwashing facilities, soap, food and water storage.