Aims: This study was conducted to investigate the inactivation kinetics of Bacillus cereus vegetative cells upon exposure to low-temperature nitrogen gas plasma and to reveal the mode of inactivation by transcriptome profiling. Methods and Results: Exponentially growing B.cereus cells were filtered and put on agar plates. The plates, carrying the filters with the vegetative cells, were placed into low-temperature nitrogen gas plasma at atmospheric pressure. After different exposure times, the cells were harvested for RNA extraction and enumeration. The RNA was used to perform whole-transcriptome profiling using DNA microarrays. The transcriptome profile showed a large overlap with profiles obtained from conditions generating reactive oxygen species in B.cereus. However, excess radicals such as peroxynitrite, hydroxyl and superoxide could not be detected using radical-specific fluorescence staining. Lack of UV-specific responses including factors involved in DNA damage repair is in line with the absence of UV-specific emission in the afterglow of the nitrogen gas plasma as analysed using optical emission spectroscopy (OES). Conclusions: Antibacterial activity of nitrogen gas plasma is not based on UV radiation. Exposure to nitrogen gas plasma leads to oxidative stress and inactivation of targeted cells. A secondary oxidative stress with the indicative formation of reactive oxygen species within cells could not be observed. Significance and Impact of the Study: This study represents the first investigation of differential gene expression on a genome-wide scale in B.cereus following nitrogen gas plasma exposure. This study may help to design economically feasible, safe and effective plasma decontamination devices.