Recent foodborne outbreaks and recalls involving Listeria monocytogenes and Salmonella-contaminated peaches have caused significant economic losses to the peach industry. This study evaluated the effectiveness of chlorine, a commonly used sanitizer in the fresh produce industry, against L. monocytogenes and Salmonella and its ability to control cross-contamination in fresh peaches. Peaches inoculated with L. monocytogenes or Salmonella (~6 log10 CFU/peach) were treated with 50–150 mg/L of free chlorine (FC, pH6.8) 24 h post-inoculation. The results revealed that chlorine had similar efficacy against L. monocytogenes and Salmonella on peaches (p > 0.05). A 30 s treatment at 50, 100, and 150 mg/L FC resulted in dose-dependent reductions (p < 0.05), achieving reductions of 0.88–0.92, 1.54–1.61, and 1.73–1.79 log10 CFU/peach, respectively. Extending the contact time to 2 min slightly but significantly enhanced the chlorine efficacy (p < 0.05). Additionally, a 30 s to 2 min exposure to chlorine with 50–150 mg/L FC resulted in a 1.05–1.43 log10 CFU/peach reduction in yeasts and molds. Tap water exposure led to substantial cross-contamination between inoculated and uninoculated fruits and processed water, with Salmonella exhibiting higher transfer rates than L. monocytogenes. The application of chlorine mitigated the cross-contamination of both pathogens but did not entirely prevent it. These findings offer valuable insights for the peach and other stone fruit industries to verify process controls.