The prevalence of diarrheal diseases in children aged from 6 to 24 months in Burkina Faso is 38%. These diarrheas may be due to the consumption of contaminated weaning food. Therefore, the microbiological quality of follow up infant flours used as supplement foods is a key-point to reduce children diseases. In this study, the microbiological safety of locally-produced infant flours was investigated. One hundred and ninety-nine (199) samples were collected mainly in retails outlets and in Recovery and Nutrition Education Centers. According to the Burkina Faso regulations, microbiological analyses were carried out for Total Aerobic Mesophilic Flora (TAMF), thermotolerant coliforms, Salmonella spp. and yeasts/molds. The bacterial and fungal isolates were identified using phenotypic and genotypic methods and the study of the production of mycotoxins was carried out from the fungal isolates. In collected samples, the TAMF count ranged from 0 to 1.8 × 106 CFU/g with a total average of 6.3 × 104 CFU/g. About 2% of the samples had a microbial load exceeding the standards (105 CFU/g). No Salmonella spp. was isolated in the final infant flours. However, the presence of Enterobacteriaceae (Klebsiella spp. Enterobacter spp. and Cronobacter spp.) was detected and molecular characterization revealed also the presence of fungal species of the genus Aspergillus spp., Penicillium spp. and Fusarium spp. Some of these species were found to produce aflatoxins, ochratoxin A and fumonisins, which are potential carcinogenic toxins. These results demonstrated the need for a preventive approach based on the application of Hazard Analysis Critical Control Point in the food industry to ensure food safety of infant flours in Burkina Faso.