Isolate characterization and comparison are central aspects in foodborne outbreak investigation and is nowadays regularly performed using whole genome sequencing (WGS). Despite its high accuracy, WGS is relatively expensive, time-consuming, and requires specific expertise for data analysis. Therefore, this study evaluates the use of Fourier-transform infrared (FT-IR) spectroscopy as rapid and cost-effective isolate typing alternative. Presumptive B. cereus was isolated from a food sample and five fecal patient samples collected after a foodborne outbreak event; 51 isolates were screened using FT-IR. The presence/absence of the cereulide biosynthesis cluster (ces) was determined by PCR and supplemented to the FT-IR spectra. The isolates were also characterized by WGS to evaluate the performance of FT-IR. 14 different strains were identified by core-genome multi-locus sequence typing (cgMLST) from WGS. Two strains were detected in the food and in four out of five patient samples, while cereulide toxin was detected in all samples. A representative set of 13 isolates was obtained (dereplication) by comparing the FT-IR spectra through three different clustering methods: hierarchical cluster analysis (HCA), principal component analysis (PCA) and linear discriminant analysis (LDA). The overall congruency of FT-IR with cgMLST in this dataset was 96.4 % (Adjusted Wallace Index). Therefore, this study demonstrates that FT-IR spectroscopy can be a useful technique in the investigation of foodborne outbreaks, especially as a first-line screening tool to reduce the number of isolates for subsequent confirmation using WGS.