In low- and middle-income countries, food may be a critical transmission route for pathogens causing childhood diarrhoea, but basic food hygiene is often overlooked in public health strategies. Characterising child food contamination and its risk factors could help prioritise interventions to reduce foodborne diarrhoeal disease, especially in low-income urban areas where the diarrhoeal disease burden is often high. This cross-sectional study comprised a caregiver questionnaire coupled with food sampling, and food preparation observations, among the study population of an ongoing sanitation trial in Maputo. The aim was to determine the prevalence of child food contamination and associated risk factors. The prevalence of Enterococcus spp., as an indicator of faecal contamination, was estimated in food samples. Risk factor analyses were performed through zero-inflated negative binomial regression on colony counts. A modified hazard analysis and critical control point approach was used to determine critical control points (CCPs) that might effectively reduce risk. Fifty-eight linked caregiver questionnaires and food samples were collected, and 59 food preparation observations were conducted. The prevalence of enterococci in child foods exceeding 10 colony forming units per gram was 53% (95% confidence interval [40%, 67%]). Risk factors for child food contamination were identified, including type of food, food preparation practices, and hygiene behaviours. CCPs included cooking/reheating of food and food storage and handling. This exploratory study highlights the need for more research into diarrhoeagenic pathogens and foodborne risks for children living in these challenging urban environments.