Salmonella has been reported to be involved in several foodborne illness outbreaks, many of which resulted from consumption of raw tomatoes. This research aimed to optimize and evaluate the concentration of free chlorine (hypochlorous acid [HOCl]) used as a sanitizer to prevent cross-contamination of tomatoes inoculated with a cocktail of five rifampin-resistant Salmonella enterica serovars in a laboratory-based model flume system. Organic load, prepared using sterilized Scotts Premium Topsoil, was added in different quantities to the flume wash water to simulate real-world packinghouse conditions. In a typical packinghouse operation utilizing a recirculating flume system, the organic matter washed from tomato surfaces accumulates over time. In this study, different concentrations (0, 25, 50, 75, and 100 ppm) of HOCl were used as sanitizers under three organic load conditions (0, 650, and 1,000 mg/L chemical oxygen demand). Results showed that 100 ppm of HOCl was necessary to prevent Salmonella cross-contamination of uninoculated tomatoes in the model flume system in the presence of organic loading. Also, when treated with 100 ppm of HOCl, Salmonella levels were reduced by >4.5 log CFU per tomato from inoculated tomatoes in the presence of organic load. At 75 ppm of HOCl, Salmonella cross-contamination was prevented, but only in the absence of organic loading. In studies in which plate counts were negative, whole tomato enrichment studies were performed. No cross-contamination of uninoculated tomatoes was recorded when 100 ppm of HOCl was used, even in the presence of high organic load (1,000 mg/L chemical oxygen demand). Although sanitizer application reduces contamination on tomato surfaces, the primary function of sanitizers in the wash water is to prevent cross-contamination.