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. Two days later, on 15 July, he officially became an Inter player, signing a four-year contract. Jonathan made his Inter debut on 11 September 2011 in week two of 2011–12 Serie A, playing the full 90 minutes in a 4–3 away loss to Palermo. 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.