On 18 August 2013, in the opening match of the 2013–14 season, against Cittadella in third round of Coppa Italia, Jonathan scored his first goal of the season after he beat goalkeeper Raffaele Di Gennaro with a header, following a cross from Fredy Guarín. Inter won the match 4–0. 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. 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. 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. One month later, Jonathan scored the opener in a 4–2 win over newly promoted Hellas Verona, that was ruled out as an own-goal. Jonathan scored for the second time in Serie A, netting the equalizer in a 1–1 away draw against Bologna on 24 November. Jonathan continued his fine form, supplying his third assist of the season in a 3–3 draw against Parma at the San Siro, assisting Rodrigo Palacio in the 44th minute of the match.