Children under-five years of age are particularly vulnerable to severe acute malnutrition (SAM), and the risk factors associated with relapse to SAM are poorly understood. Possible causes are asymptomatic or symptomatic infection with enteric pathogens, with contaminated food as a critical transmission route. This cross-sectional study comprised a household survey with samples of child food (n=382) and structured observations of food preparation (n=197) among children aged 6-59 months that were discharged from treatment in community management of acute malnutrition (CMAM) programmes in Aweil East, South Sudan. We quantified Escherichia coli and total faecal coliforms (TFCs), measured in colony forming units per g of food (CFU/g), as indicators of microbial contamination of child food. A modified hazard analysis critical control point (HACCP) approach was utilised to determine critical control points (CCPs) followed by multivariate logistic regression analysis to understand the risk factors associated with contamination. Over 40% of samples were contaminated with E. coli (43% >0 E. coli CFU/g, 95%CI 38-48%), and 90% had >10 TFCs (CFU/g) (>10TFC CFU/g, 95%CI 87-93%). Risk factors associated (p<0.05) with child food contamination included if the child fed themselves (95% CI 1.16, 3.44, log[odds] = 2.20), exposure to animals (95% CI 0.28, 1.68, log[odds] = 0.97), and protective factors for contamination included feeding with a spoon (95% CI -7.81, -1.54, log[odds] = -4.17). This study highlights strategies that can support interventions that reduce food contamination exposure in young children and help further protect those that are highly vulnerable to recurrent exposure to diarrhoeagenic pathogens.