► Phenolic compounds were compared between bagged and unbagged apple fruits. ► Fruit bagging lowered the phenolic compound concentrations in apple peels. ► Fruit bagging affected the phenolic compounds in apple flesh. ► The effects of bagging treatment differed among varieties. Concentrations of eighteen types of phenolic compounds were compared between bagged and unbagged fruits in both the peel and the flesh of three apple cultivars, ‘Golden Delicious’, ‘Red Delicious’, and ‘Royal Gala’. Fruit bagging treatment significantly lowered the phenolic compound concentrations in apple peels, except the gallic acid and chlorogenic acid in ‘Red Delicious’. Among the detected phenolic compounds in fruit peels, anthocyanins were the most sensitive to fruit bagging, followed by flavonols. In apple flesh, chlorogenic acid, phloridzin, and flavanols were the major phenolic compounds. The concentration of chlorogenic acid in apple flesh was hardly affected by the bagging treatment. Fruit bagging did not affect the concentration of phloridzin in the flesh of ‘Golden Delicious’, but the treatment enhanced the content of the compound in ‘Red Delicious’ and reduced the concentration in ‘Royal Gala’. The flavanols concentration was reduced by the bagging treatment in the flesh of ‘Golden Delicious’ and ‘Red Delicious’, but remained unchanged in the flesh of ‘Royal Gala’. The concentration of total phenolics was higher in apple peel than in the flesh, except that chlorogenic acid was significantly higher in the flesh of either bagged or unbagged ‘Red Delicious’ and unbagged ‘Royal Gala’. Generally, fruit bagging treatment decreased most of the phenolic compound concentrations in both the peel and the flesh, especially those in peels. The effect of bagging treatment differed among cultivars.