Pepe was operated on 27 February 2013, and after a few matches with the youth squad he returned to the pitch on 18 December, coming on as an 81st-minute substitute of a 3–0 win over U.S. Avellino 1912 in the Coppa Italia. He was injured again in mid-February 2014, and was finally called up again for Juventus's League match with Bologna F.C. 1909 on 19 April, making his third appearance of the season in a 3–0 success against Cagliari that confirmed the "Old Lady"'s third consecutive national championship conquest.