: Dormant Bacillus cereus spores can initiate foodborne illnesses upon germination, posing a significant threat to food safety. Emerging plasma technology exhibits limited efficacy in inactivating highly resistant spores, however, it significantly inhibits spore germination, although the underlying mechanism remains unclear. This study aimed to elucidate the inhibitory mechanism of atmospheric pressure plasma jet (APPJ) on spore germination through comprehensive analysis of protein expression and functional alterations during the germination process following APPJ treatment. The results indicated that 2.45 log CFU of dry spores on stainless steel can be inactivated after 20 min of APPJ treatment. Notably, APPJ-treated spores failed to respond to the nutrient and non-nutrient germination, suggesting a potential impairment of the germination receptors. Furthermore, APPJ treatment significantly downregulated the expression of proteins involved in spore structure, amino acid metabolism, energy production, DNA replication and repair, ultimately hindered spore germination and growth. This study elucidated the mechanism by which plasma inhibited the germination of Bacillus cereus spores deposited on stainless steel from multiple dimensions. The research findings can provide a theoretical foundation for the application of plasma technology in bacterial spore inactivation.