Diarrhoeal disease remains a significant cause of mortality among children under five, particularly in high-burden settings where food consumed by young children is frequently contaminated. Understanding food preparation, feeding, and storage practices for children aged 6–24 months is essential to inform interventions that reduce diarrhoeal disease. Using the Hazard Analysis and Critical Control Points (HACCP) approach, we identified critical control points (CCPs) associated with potential food contamination among households with a child aged 6–24 months in the Polana Caniço neighbourhood of Maputo, Mozambique. We conducted 110 structured observations of household food hygiene practices, including food handling, preparation, cooking, feeding, and storage, to identify key hazards and CCPs for microbial contamination of foods consumed by young children. Food flow diagrams were developed for the main food groups to support the HACCP analysis. Our systematic assessment of food hygiene behaviours identified several key practices to target: cleaning utensils used for child feeding, caregiver handwashing with soap before feeding, boiling liquids added to food, storing cooked food in clean containers, and thoroughly cooking and reheating food before feeding. While these CCPs are consistent with those identified in similar settings, our findings provide context-specific evidence on food hygiene practices in an urban informal setting. These findings can inform future research to evaluate the relative importance of identified hazards and CCPs and guide policymakers and practitioners in designing household- and community-level interventions to reduce foodborne health risks among young children.