A strong and quick right-back capable of running at pace with the ball. As well as being a skilful dribbler he also has a powerful right-footed shot. Equally at home with attacking and defensive duties. After making his debut for Cruzeiro on 25 September 2007 he joined Santos at the end of 2010, before making the move to Europe and Inter in July 2011.

Cruzeiro
Jonathan made his debut as professionist in the Campeonato Brasileiro for Cruzeiro against Santos in a 3–2 home win on July 24, 2005. He scored his first goal as professionist against Corinthians in a 3–0 away win on August 25, 2007.

Santos
In December 2010, Jonathan signed by Santos for €2 million (with Cruzeiro retained 50% registration rights). Santos paid €1.2 million to acquire 30% while Santos's investment partner Terceira Estrela Investimentos S/A (TEISA) acquired 20% for €800,000. He signed a 4-year contract with €15 million release clause. With Santos, he won Campeonato Paulista and Copa Libertadores.

Inter
On 13 July 2011, it was announced that Jonathan would leave Santos to train with Serie A giants Internazionale, pending the finalization of the transfer. Two days later, on July 15, he officially became an Interazionale player and signed a four-year contract. In January 2012, he moved to Parma on loan until the end of the season and established himself as the team's regular right wing-back. After played for Parma in the last round, Jonathan returned to Milan and was included in the 20-men squad to Indonesia . In the play offs of the Euro league, he played the two legs against Hajduk.