The microbial quality of food contact surfaces in the food preparation facilities is an indication of their hygiene status. The objective of this study was to assess the hygiene status and the incidence of pathogens of food contact surfaces in the food preparation facilities of schools offering school feeding programs in the Mpumalanga Province, South Africa. 192 swab samples were collected by swabbing 100 cm2 areas of food contact surfaces in the food preparation facilities of randomly selected schools. Only 16.2% of the food contact surfaces had satisfactory hygiene status in which the surface aerobic colony counts were less than 2 log cfu/cm2. Only 3% and 6% of the benchtop and dry storage surfaces respectively had a satisfactory hygiene status. Listeria monocytogenes and Staphylococcus aureus were the most detected pathogen on food contact surfaces with 53.1% and 25.5% incidences. There was a strong significant positive correlation between the occurrence of L. monocytogenes on dry storage surfaces and benchtop (rho = 0.539**, p = 0.01), cutting board (rho = 0.541**, p = 0.01), refrigerator handle (rho = 0.420*, p = 0.05), and sink faucet (rho = 0.498**, p = 0.01) surfaces. The Bacillus species was generally detected the most from aerobic growth isolates of food contact sources, among which Bacillus subtilis was the most abundant species identified. Most of the food contact surfaces in the food preparation facilities of schools offering school feeding programs were of unsatisfactory hygiene status and constituted a food safety risk to schoolchildren consuming meals at school.