Bacillus cereus spores pose a challenge to the food industry owing to their ability to germinate in food during storage and produce toxins. The objective of the current study was to investigate the effect of pulsed electric field (PEF) at low electric field strength (i.e., 7.3, 8.1, 8.8 and 9.4 kV/cm) and moderate temperatures (65, 70, 75 and 80°C) on B. cereus spores. PEF treatment at 9.4 kV/cm at 80°C (pulse width of 20 μs and frequency of 300 Hz) led to a 3.1 log CFU/ml reduction in the number of B. cereus spores and importantly, the D88°C values of the surviving spores were reduced by 12 min. Differential gene expression revealed the upregulation of the gene (BC1768) encoding for chitooligosaccharide deacetylase involved in peptidoglycan degradation in PEF treated spores. The gene (BC2729) encoding for a penicillin-binding protein required for septation during sporulation was downregulated in PEF treated spores. Practical applications PEF treatment is an emerging food processing technology that has gained attention owing to its potential to provide high-quality foods. However, to date the inactivation of bacterial spores by PEF has only been partially successful and then only when combined with high heat. The effect of PEF on the thermal stability of spores has not previously been reported. The current work bridges these gaps by providing insight into differential gene expression associated with the PEF treatment of B. cereus spores. The study indicates the potential for PEF to be incorporated into a hurdle regime targeting spore inactivation and provides data on specific genes that may help to provide a better understanding of the stress induced in B. cereus spores by PEF treatment.