The use of secondary quality produce has gained attention as a solution to food waste in both the U.S. and Europe. The purpose of this study was to evaluate the impact of using secondary quality or outgraded produce on the retention of surface inoculated E. coli following a rinse treatment on four model fresh produce systems (apple, tomato, carrot, lettuce). A three-strain cocktail of rifampicin-resistant generic E. coli, with a concentration of 9.0 log CFU/mL, was spot-inoculated on the intact surfaces of U.S. No.1 grade produce items and damaged or decayed areas of outgraded produce items. Generally, outgraded produce of all four kinds retained higher levels of inoculated E. coli following two postharvest treatments, chlorinated (150 ppm) or water only. However, physical damage, those defects which compromised the integrity of the produce surface, lead to significantly greater E. coli levels following rinsing than did physiological defects. Compared to U.S. No.1 quality apples, outgraded apples retained 4.3 ± 1.4 log CFU/g more E. coli following water only treatment, and 3.6 ± 1.7 log CFU/g more following chlorine treatment. Outgraded tomatoes retained significantly more (3.5 ± 1.1 log CFU/g) inoculated E. coli following water only rinse and 3.0 ± 1.4 log CFU/g more inoculated E. coli following chlorine treatment than U.S. No.1 quality tomatoes did under the same treatment conditions. Outgraded carrots retained 1 ± 1.1 log more CFU/g inoculated E. coli following water only treatment and 0.5 ± 0.8 log more CFU/g inoculated E. coli following chlorine treatment, compared to U.S. No.1 carrots. Outgraded lettuce leaves retained 1.6 ± 0.5 log CFU/g more inoculated E. coli following water only treatment and 4.1 ± 0.4 log CFU/g more inoculated E. coli following chlorine treatment than did U.S. No.1 quality lettuce leaves under the same treatment conditions. Treating with 150 ppm chlorine was not sufficient to eliminate the increased microbial retention associated with secondary quality or outgraded produce, and the efficacy of disinfection was greatly affected by type of defect. Apples with physical damage retained significantly higher E. coli loads than did those with physiological defects, an additional 2.6 log CFU/g under chlorine treatment and 0.8 log CFU/g more under was water only treatment. Tomatoes with physical damage had a 1.3-log CFU/g and 0.6-log CFU/g average increase of retained E. coli counts compared to those with physiological defects following a chlorine and water only treatment, respectively. Although a chlorine dip provided only a modest reduction in pathogens, generally, outgraded produce with physiological defects may present less food safety risks if introduced into the fresh market than does produce with physical damage due to their enhanced retention of bacterial cells. Therefore, as industry considers how to minimize its food waste problem, preferentially directing physically damaged produce away from the fresh market will help to minimize risk while maximizing food resources.