In this study, we report on the epidemiologic investigation in a Swiss powdered infant formula production facility after a batch of Powdered Infant Formula (PIF) was found to be contaminated with Cronobacter (C.) sakazakii during a routine testing of packed products of a Swiss PIF brand ready for distribution. Epidemiological investigation on isolates originating from PIF batches from the production unit by macro restriction typing quickly (PFGE) identified an isolate showing a pattern identical to the ones originating from the packed product, suggesting this strain being the source of contamination. To obtain an overview on the heterogeneity of strains isolated within this production unit 115 C. sakazakii isolates, which were routinely collected between August 2015 and September 2016, were characterized by PFGE and serotyping. In addition, Multilocus Sequence Typing (MLST) was performed on 11 selected isolates. Macro restriction analysis revealed the presence of two main clusters (C1,C2) containing multiple isolates from various sources and time points with the oldest isolates dating back to October and August 2015 respectively. Of interest, within both clusters isolates were identified showing identical PFGE patterns but different serotypes. Moreover, MLST analysis on selected isolates revealed that isolates showing identical PFGE types may exhibit different MLSTs and/or serotypes. Our data suggest that application of one of the latter two typing methods bears the risk that strains may incorrectly be considered “epidemiologically unrelated”. Based on these results the application of PFGE using the primary (and the secondary) restriction enzyme is recommended for trace back studies.