Cronobacter sakazakii in powdered infant formula is extremely harmful to infants. While hygienic standards for infant formula have imposed a strict limit for this microorganism, Cronobacter sakazakii-tainted baby formula incidents continue to occur. There are many factors that contribute to the occurrence of Cronobacter sakazakii in the production line of powdered infant formula. This article describes the characteristics of spatial exposure of powdered infant formula to Cronobacter sakazakii during the production process, focusing on the adverse effects on the monitoring and removal of Cronobacter sakazakii residues caused by hidden contamination associated with the stress-tolerant phenotype and viable but non-culturable (VBNC) phenotype in Cronobacter sakazakii. The advantages and disadvantages of the existing detection technologies for Cronobacter sakazakii are discussed, highlighting the importance of detection sensitivity, recovery and identification of VBNC cells in the control of hidden contamination. It is hoped that this review will provide new ideas for the monitoring and prevention of Cronobacter sakazakii during infant formula production.