Background Safe complementary food is food that will not cause harm to infants and children when prepared and fed as recommended. Unfortunately, children are frequently suffering from diarrhoea which is not only preventable but is also largely attributed to complementary foods hence this study.   Methodology The study was carried out in 2015 in Adyel Division, Lira District among caregiver-child pairs. The children were between the ages of 6 – 23 months. Information collected was about the children’s diarrhoeal patterns, nutritional status, and complementary food safety. Results Analyses of food samples revealed that freshly cooked food was contaminated with fecal coliforms (4.88±1.87 log cfu/g), and the levels of fecal coliforms in stored food increased with prolonged storage period (5.49b±1.86 log cfu/g).  Drinking water too was contaminated with E.coli (2.86 logs cfu/ml). Water in storage containers had total coliform counts of up to 3.14 log cfu/ml. In over half of the households (56.7%), the microbial counts in household drinking water containers (4.48E+03cfu E.coli) were more than those found at the respective water sources (4.46E+02cfu E.coli). Water treatment accounted for 25% of the variation (p=0.005) in E.coli counts in drinking water that was found in water storage containers. About 32.5% of the frequency or recurrence of diarrhea episodes in two weeks among children was explained by the presence of fecal coliforms in freshly cooked complementary food (p=0.001). Overall, diarrheal infections (p=0.030), inappropriate child-feeding practices (p=0.048), and poor hand-washing (p=0.011) played a significant role in influencing child health.  Conclusion The food safety in this study was compromised by poor complementary food handling practices. Recommendation There is a need to study specific food combinations under more controlled conditions to compare the effect of the different handling practices on the microbial load in the various foods.