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<i>Salmonella</i> Enteritidis (<i>S.</i> Enteritidis) can adapt to sublethal sodium hypochlorite conditions, which subsequently triggers stress resistance mechanisms in this pathogen. Hence, the current work aimed to reveal the underlying stress adaptation mechanisms in <i>S.</i> Enteritidis by phenotypic, proteomic, and physiological analyses. It was found that 130 ppm sodium hypochlorite resulted in a moderate inhibitory effect on bacterial growth and an increased accumulation of intracellular reactive oxygen species. In response to this sublethal treatment, a total of 492 proteins in <i>S.</i> Enteritidis showed significant differential abundance (<i>p</i> < 0.05; fold change >2.0 or <0.5), including 225 more abundant proteins and 267 less abundant proteins, as revealed by the tandem-mass-tags-based quantitative proteomics technology. Functional characterization further revealed that proteins related to flagellar assembly, two-component system, and phosphotransferase system were in less abundance, while those associated with ABC transporters were generally in more abundance. Specifically, the repression of flagellar-assembly-related proteins led to diminished swimming motility, which served as a potential energy conservation strategy. Moreover, altered abundance of lipid-metabolism-related proteins resulted in reduced cell membrane fluidity, which provided a survival advantage to <i>S</i>. Enteritidis. Taken together, these results indicate that <i>S.</i> Enteritidis employs multiple adaptation pathways to cope with sodium hypochlorite stress.