Chicken meat is frequently contaminated with zoonotic bacterial pathogens such as Campylobacter spp and Salmonella spp. These two bacterial genera are commonly linked with cases of human gastrointestinal disease, thus mitigating their presence in the poultry meat supply chain is paramount. Here, the efficacy of two sanitizers, peroxyacetic acid (PAA) and acidified sodium chlorite (ASC), was tested using whole chicken carcasses obtained either prior to the inside/outside wash or post-immersion spin chill steps of processing. Two concentrations of PAA (100 and 200 ppm) and ASC (450 and 900 ppm) were tested and compared with chlorine. All sanitisers significantly reduced total viable bacteria and Campylobacter counts per carcass. The prevalence of Salmonella was also reduced. Log reduction of both the total viable and Campylobacter counts were, however, temperature and processing stage dependent. The survivability and virulence of sub-lethally injured bacteria after exposure to sanitisers, however, is poorly understood. We also investigated the survivability and invasion potential of Campylobacter jejuni and Salmonella Typhimurium following exposure to chlorine and acidified sodium chlorite (ASC) during storage in chicken meat juice (CMJ). Campylobacter jejuni and Salmonella Typhimurium were stored in CMJ under refrigeration (5°) following exposure to either chlorine or ASC. Bacterial culturability, motility, and invasive capacity were characterised. Changes in the expression of Campylobacter and Salmonella specific stress response and virulence genes were also investigated. CMJ facilitated the survival of both Campylobacter and Salmonella following exposure to chlorine but not ASC. Both chlorine and ASC reduced bacterial invasiveness, motility, and culturability of Campylobacter jejuni but not Salmonella Typhimurium. Bacterial stress response and virulence genes in Campylobacter jejuni (ropB, sobB, flaG, flaA, cadF, racR) or Salmonella Typhimurium (rpoH, rpoS, hilA, fimH, spvR, avrA) were upregulated over time indicating an increase in virulence potential. This study indicates that sub-lethally injured Campylobacter jejuni and Salmonella Typhimurium in CMJ remain a significant risk in the food chain due to the likelihood of cross-contamination while handling chicken meat.