During the 2012–13 season, Juan Jesus emerged as part of Inter's first choice starting XI, featuring alongside Andrea Ranocchia and Walter Samuel in a 3–5–2 system. He scored his first goal on 19 May 2013 in a 2–5 home defeat against Udinese, the last match of the domestic season. He ended the year with 44 appearances in all competitions, including 31 in Serie A with Inter, who finished the season in a disappointing ninth place and failed to qualify for either next season's UEFA Champions League or UEFA Europa League.