On 13 July 2011, it was announced that Jonathan would leave Santos to train with Serie A giants Inter Milan, pending the finalization of the transfer.

[10] Three days later Jonathan made his Champions League debut, playing the entire match on Matchday 1 against Turkish side Trabzonspor in a 0–1 loss at the San Siro.

[17] On 21 April, Jonathan assisted Tommaso Rocchi for the only goal of the match against Parma, which was scored in 82nd minute, salvaging the club's hopes for qualifying for Europe.

For this disappointing position, Stramaccioni was sacked and replaced by Walter Mazzarri, where Jonathan secured a more regular place at starting lineup.

[23] In first match of the new season in Serie A, Jonathan assisted the first goal of Yuto Nagatomo in a 2–0 win over against Genoa, helping the team to make a fine start.

[24] In second match on 1 September, Jonathan made his second assist of the season by providing the pass for Rodrigo Palacio opening goal of the 3–0 away win against Catania.

[25] On 26 September, Jonathan scored his first league goal with Inter in a 2–1 win at San Siro against Fiorentina, giving his team the advantage in the 83rd minute after a powerful shot from inside the box.