A cultivar (Malus domestica cv. Fuji) of apple was selected to make apple peel (AP) powder by three different powdering methods. Frozen AP was thawed and subsequently was dried or ground without drying. After AP was dried by hot-air drying at 60°C or freeze-drying, the dried AP was ground using a conventional blender. Separately, the thawed AP was powered by using a cryogenic micro grinding technology (CMGT). The ground AP and three types of AP powder were extracted using deionized water, 20, 40, 60, 80, or 100% methanol, followed by vacuum evaporation. The total phenolics contents (TPC), total flavonoids contents (TFC), DPPH, and ABTS radical scavenging capacities of each extract were compared to determine an efficient powdering method. Lyophilized AP powder extract using 60% methanol showed the highest TPC and DPPH radical scavenging capacity. In contrast, 60% methanol extract of the powder by CMGT, resulting in the smallest particle, exhibited the highest TFC and ABTS radical scavenging capacity. This study suggests that the extraction yield of bioactive compounds from AP may be varied according to different powdering methods and that a new powdering process such as CMGT may be applicable to develop functional foods efficiently.