Environmental harborage of the foodborne pathogens Listeria monocytogenes and Salmonella enterica in food processing facilities remains a challenging issue in the safe production of food. Once these pathogens enter a food processing environment they may persist for extended periods of time despite routine cleaning and sanitation operations. Persistence may be mediated by genetic determinants (such as stress adaptations) or more simply by the presence of niches in the environment that are difficult to clean. Prolonged presence of these pathogens in the food processing environment increases the risk of their cross-contamination into food products. Indeed, many epidemiological investigations have linked outbreaks of foodborne illness to environmental contamination from the food processing environment. This collection of works aims to address this issue by providing evidence-based recommendations for the environmental cleaning and sanitation of food processing environments. In chapter 2, we analyzed the genomes and metadata of 4,969 Listeria monocytogenes isolates collected from U.S. food processors. We found that sanitizer tolerance genes and other environmental stress adaptations were common but didn’t find evidence for their contribution to environmental persistence. These findings do not support the conclusion that food processing facilities should change their sanitation strategies based on the presence of sanitizer tolerance genes or other stress adaptions in Listeria monocytogenes, but changes in hygienic design of equipment and niche removal may be more broadly effective at limiting environmental persistence. In chapter 3, we built a simulation model to quantify the cross-contamination of Salmonella into milk powder from the processing environment. We found that dry wiping of the surface with a towel, and flushing the surface with product, resulted in meaningful reductions in the number of contaminated products. This work supports the use of these interventions in dry processing environments as a part of routine cleaning operations or directly after a suspected contamination breach. Additionally, this work identified Enterococcus faecium and Listeria innocua as dry cleaning surrogates representative of Salmonella in different cleaning scenarios through the use of modeling. In chapter 4, we assessed the efficacy of visual inspection as a cleaning verification activity and found that the use of flashlights, food safety trainings, tactile inspection, and frequent angle changing improved the effectiveness.