Diarrhoeal disease remains a leading cause of death in children in sub-Saharan Africa, attributed to environmental health factors such as inadequate water, sanitation and hygiene (WASH) and food hygiene. This formative study in low-income areas of Blantyre focussed on the practices in Early Childhood Development Centre (ECDCs) environments where children spend a significant amount of time. A mixed-methods approach was applied to identify key hygiene behaviours in ECDCs through; checklist and structured observations (n = 849 children; n = 33 caregivers), focus group discussions (n = 25) and microbiological sampling (n = 261) of drinking water, food handler’s hands, and eating utensils. ECDCs had inadequate WASH infrastructure; coupled with poor hygiene practices and unhygienic environments increased the risk of faecal-oral disease transmission. Presence of E. coli in drinking water confirmed observed poor water handling habits by staff and children. Addressing undesired hygiene practices in ECDCs has the potential to improve the health outcomes of children in low-income settings.