He made his debut on the first team in 2010, winning the 2010 Copa Libertadores, and in December 2011, the club sold him for about R$9.26 million[1] (reported €3.8million fee); 65% of the economic rights of Juan went to his agent, Giuliano Bertolucci[2] and 35% to third-party owner DIS Esporte.

[8] 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.

[12][13] Juan Jesus made his 100th appearance for Inter on 4 February 2015 in a game against Napoli in the quarter-finals of the Coppa Italia, which the Nerazzurri lost 1–0 away at Stadio San Paolo thanks to a late winner by Gonzalo Higuaín.

[16] The purchase obligation was activated during the 2016–17 season, meaning that Jesus would join Roma on a permanent deal in the summer transfer window.

[20] Juan Jesus started in the centre of defence, alongside captain Thiago Silva, in all of Brazil's matches at the 2012 London Olympics, helping the nation to a silver medal.