The effects of pulsed electric fields (PEF, 0.008–1.3 kJ kg−1) on the total phenolic, flavonoid and flavan-3-ol contents, as well as on the antioxidant capacity of apples stored at different temperatures (4 and 22 °C) along 48 h were studied. Contents of phenolic compounds observed in PEF-treated apples were higher than those of untreated. The mildest PEF treatment (0.008 kJ kg−1) produced the maximum increases of total phenolics (13%) and flavan-3-ol (92%) contents in apples stored during 24 h at 22 °C, while it was observed at 4 °C for flavonoids (58%). On the other hand, the antioxidant capacity of apples was enhanced by 43% respect to that of untreated with the mildest PEF treatment after 12 h at 4 °C and by 15% after 24 h at 22 °C. Therefore, PEF technology could be used to increase the antioxidant potential of apples by controlling treatment and storage conditions.