•Responses of phenolics to fruit bagging and the following bag removal were studied.•Fruit bagging lowered the phenolic compounds concentration in apple peels.•The bag removal increased the concentrations of most phenolic compounds.•The compounds responded differently to fruit bagging and the following bag removal. During the course of fruit development, the concentration of cyanidin-3-galactoside decreased in the peel of unbagged ‘Golden Delicious’ apples but increased in that of ‘Red Delicious’ apples. Fruit bagging completely inhibited the synthesis of cyanidin-3-galactoside in fruit peel. After re-exposure to sunlight for 9 days, ‘Golden Delicious’ synthesized an increased amount of anthocyanin compared to previously unbagged fruit, whereas ‘Red Delicious’ synthesized less than control. The concentration of quercetin-3-glycoside was also reduced during bagging treatment from the early developmental stage, but was enhanced after removing bags late in fruit development. However, the synthesis of the six types of flavonols, quercetin-3-galactoside, quercetin-3-glucoside, quercetin-3-rhamnoside, quercetin-3-rutinoside, quercetin-3-xyloside and quercetin-3-arabinoside, might possess different sensitivities to bagging treatment, as their concentrations increased at different levels compared to control. Chlorogenic acid in ‘Red Delicious’ apples and procyanidin B1 in ‘Golden Delicious’ had no response to bagging treatment while the former compound in ‘Golden Delicious’ and the latter in ‘Red Delicious’ did respond, suggesting that the regulation of the synthesis of these compounds by sunlight irradiation might be genotype dependent. Meanwhile, the response of other types of phenolic acids and flavanols as well as phloridzin to the bagging treatment was similar; their concentrations decreased with fruit bagging and then increased after bag removal, indicating that their synthesis regulation might be genotype independent.