Background <p>Powdered infant formula is issued in instances where breastfeeding is not possible or inadequate as a substitute, but it is not a sterile product and is sometimes a vehicle for certain pathogens like Cronobacter sakazakii with neonatal deaths reported to occur in 40–80% of cases. Therefore, the aim of this study was to determine the microbial quality and safety of powdered infant formula for infants below six months of age using indicator organisms, and foodborne pathogens.</p> Methods <p>A cross-sectional study was conducted on 106 Powdered Infant formula milk samples to assess the microbial safety and quality using mesophilic aerobic colony count, Enterobacteriaceae, coliforms counts and pathogens Salmonella species and Cronobacter sakazakii using ISO and NMKL-Nordval International methods.</p> Results <p>Mesophilic aerobic counts were detected in 9.4% (<i>n</i> = 20) of the samples. Enterobacteriaceae and total coliforms were detected in 9.4% (<i>n</i> = 10) and 7.5% (<i>n</i> = 8). Cronobacter sakazakii were also detected, with a prevalence rate of 5.6% (<i>n</i> = 6/107), and no <i>Salmonella</i> species were detected in this study.</p> Conclusion <p>The study on powdered infant formula (PIF) concludes that while the majority of the formulas met microbial quality and safety standards, a notable percentage contained mesophilic aerobic colonies, Enterobacteriaceae, and coliforms, with Cronobacter sakazakii present in 5.6% of them. This finding highlights a potential health risk for infants under six months, especially given the reported high mortality rate associated with Cronobacter sakazakii infections. However, no Salmonella species were detected. The results underline the importance of stringent microbial quality controls and handling practices for PIF to safeguard infant health.</p>