Controlling water quality is critical in preventing cross-contamination during fresh produce washing. Process wash water (PWW) quality can be controlled by implementing chemical disinfection strategies. The aim of this study was to evaluate the pilot-scale efficacy of chlorine dioxide (ClO2) during processing on the reduction of Escherichia coli in the PWW and on processed fresh-cut ‘Lollo Rossa’ lettuce. The objective was to have a residual target concentration of either 5 or 3 mg/L ClO2 in the washing tank (3.5 m3) before and during 800 kg of lettuce processing (90 min). After 90 min., a nonpathogenic, non-Extended Spectrum Beta-Lactamase (ESBL) E. coli inoculum from an overnight culture broth (37 °C) was added to the tank resulting in an approximate final level of 106 CFU/mL. PWW and lettuce samples for microbiological and chemical analyses were taken before and after the input and supply halted. ClO2 concentrations quickly decreased after ClO2 input halted, yet a residual concentration of ≥2.5 mg/L and ≥2.1 mg/L ClO2, respectively for 5 and 3 mg/L pilots, was present 12 min after the supply halted. No detectable levels of E. coli (limit of detection 5 log) were determined in the water within 1 min after E. coli was added to the ClO2 containing wash water. Results demonstrated that ClO2 use at the semi-commercial pilot scale was able to reduce the E. coli peak contamination in the PWW. After storage (5 days, 4 °C), background microbial communities (i.e., fluorescent Pseudomonads and total heterotrophic bacteria) grew out on lettuce. Overall, ClO2 decreased the potential for cross-contamination between batches compared to when no sanitizer was used. Chlorate levels of the lettuce sampled before entering the wash water ranged from 7.3–11.6 μg/kg. The chlorate levels of the lettuce sampled after being washed in the ClO2 containing wash water, as well as after rinsing and centrifugation, ranged from 22.8–60.4 μg/kg; chlorite levels ranged from 1.3–1.6 mg/kg, while perchlorate levels were below the limit of quantification (LOQ, <5 ng/g). In this study, we report the semi-commercial pilot-scale evaluation of ClO2, for its ability to maintain the PWW quality and to prevent cross-contamination in the washing tank during fresh-cut lettuce processing. Furthermore, we provide quantitative values of ClO2 disinfection by-products chlorate and chlorite as well as of perchlorate from PWW and/or lettuce samples.