It is commonly believed within the citrus industry that handling, waxing, and storage of navel oranges may have undesirable effects on flavor. However, the effect of each potential influencing factor under commercial conditions is not completely understood. The purpose of this study was to systematically investigate these potential influences on navel orange flavor. Navel oranges were harvested on two separate dates, using three grower lots per harvest date, and the fruit run on a commercial packing line. Fruit were sampled at four different stages of the packing process: in the field bin; after the washer; after the waxer; and after packing into standard cartons. Fruit quality, flavor, and juice ethanol concentration were evaluated immediately after sampling and following 3 and 6 weeks of storage at 5 °C. The overall hedonic score, a measure of flavor, significantly declined from 6.5 to 5.7, as a result of 6 weeks storage. Fruit selected from field bins, from after the washer, and after the waxer were all judged by the taste panel to be equivalent in flavor. The packed fruit were judged to be slightly inferior in flavor. Titratable acidity declined while soluble solids increased as a result of storage; the stage of the packing process influenced neither. Waxing and storage both were associated with higher ethanol levels in the fruit.