Identification and quantification of the major polyphenols, and antioxidant activity (AOA), in the peel of apple varieties, Granny Smith (GS) and Gold Rush (GR), during storage and over two growing seasons (2011 and 2012) were examined. GR had higher amount of flavan-3-ols, dihydrochalcones, and flavonols compared to GS. Of all polyphenolic groups, flavonols were the most influenced by the climacteric conditions during the growing season. The higher amount of phenolic acids was detected in 2012 for the both apple varieties. Dihydrochalcones were influenced more by the variety than by the climacteric conditions during growing season. Changes in polyphenol content (TPC) and AOA during storage depended on the variety. Samples of apple peel powder, after storage, preserved the most of the antioxidants and functional properties, suggesting that apple peel powder may be used in a various food products to add phytochemicals and promote good health.