In December 2010, Jonathan signed with Santos for €2 million. Santos paid €1.2 million to acquire 30% while Santos's investment partner Terceira Estrela Investimentos S/A acquired 20% for €800,000. He signed a 4-year contract with €15 million release clause. He won Campeonato Paulista and Copa Libertadores with Santos.
On 13 July2011, 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.
In January 2012, Moreira moved to Parma on loan until the end of the season where he established himself as the team's regular right wing-back. He debuted with the club on 28 January, coming on as a substitute at half time in place of Brandão in a 1–1 draw against Catania. He scored his first goal with Parma on 11 April 2012 in a 2–0 win at Stadio Ennio Tardini against newly promoted Novara. He helped Parma to finish the season in 8th place.
Return to Inter
After playing for Parma in the final round, Moreira returned to Milan and was included in the 20-men squad to Indonesia and playing in both exhibition matches. In the playoffs for the Europa League, he played the two legs against Hajduk Split. On 17 April, Moreira scored his first goal for the Nerazzurri in the second leg of the Coppa Italia's semi-final in San Siro against Roma. The match ended 2–3 for the visitors with Jonathan scoring Inter's first goal after a back heel assist by Tommaso Rocchi. 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. At the end of the season, Inter finished 2012–13 Serie A in a disappointing 9th place, which meant they failed to qualify for either UEFA Champions League or UEFA Europa Leaguefor the first time since 1999-2000. For this disappointing position, Stramaccioni was sacked and replaced by Walter Mazzarri, where Jonathan secured a more regular place at starting lineup. 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.
Jonathan has represented Brazil at under-17 level, playing in 2003 FIFA U-17 World Championship. Brazil reach in final where Jonathan played full 90 minutes and helped Seleção beat Spain in a 1–0 win. Jonathan has never been capped at senior level for Brazil, which leaves the door open for either a Brazilian or Italian call-up.
