Barcelona 2008–09 season In the 2008–09 season, Dos Santos was in Juvenil A where he was captain of the team. During that same season, he obtained a Spanish passport and thereby acquired
Citizenship of the European Union, which enabled him to play in the first team.
2009–10 season In the summer of 2009, Dos Santos was selected by
Barcelona B manager
Luis Enrique to form part of the second team. Subsequently,
Pep Guardiola called him up to the first team during pre-season in England and the tour in the United States. On 15 August 2009, Dos Santos was called up for his first official game with the first team in the
Supercopa de España against
Athletic Bilbao, although he was eventually ruled out and saw the game as a spectator. He made his debut with Barcelona B on 5 September 2009 against
Mallorca B. The match finished in a 1–1 draw. Dos Santos made his debut for Barcelona on 28 October 2009, coming on as a substitute for
Seydou Keita in the 80th minute in an away
Copa del Rey match against
Cultural Leonesa, which Barcelona won 2–0. He made his
Champions League debut for Barcelona on 24 November 2009 against
Internazionale in a 2–0 win at the
Camp Nou when he replaced
Andrés Iniesta in the 92nd minute. Due to the lengthy
2009–10 season, many Barcelona first-team players were given breaks towards the end of the year. This meant the first team was going to be a few men short, and hence four Barça B players were called up by Guardiola on 29 December 2009. Among these four were Dos Santos,
Thiago,
Gai Assulin and
Víctor Vázquez. His La Liga debut came on 2 January 2010 when he started against
Villarreal, before being substituted by Iniesta in the 60th minute.
2010–11 season Dos Santos was called up by Pep Guardiola to the Barcelona first team during pre-season along with other players from Barcelona B. In the first three matches, Guardiola played him as defensive midfielder, a position he had never played before. Nevertheless, Dos Santos said: "I've felt comfortable in this position."
2011–12 season On 26 July 2011, Dos Santos started, and scored a goal, in the 2–2 draw against
Internacional in the
2011 Audi Cup. The match went to a penalty shootout, where he scored as well. Barcelona advanced to the final, where they beat
Bayern Munich 2–0. He was part of the starting line-up in both matches, though he played at
right back in the final. He made his season debut on 29 August in the 5–0 home win against Villarreal, coming in as a substitute for
Cesc Fàbregas in the 70th minute. On 24 November 2011, Dos Santos signed a contract extension which would keep him at Barcelona until 2015. On 6 December, he appeared in the starting squad and played 58 minutes against
BATE for the
2011–12 UEFA Champions League group stage match.
2012–13 season Despite rumours of a transfer to other Spanish clubs such as
Real Betis and
Málaga, and
Sevilla, newly appointed coach
Tito Vilanova officially called up Dos Santos to Barcelona's first team squad, handing him the number 12 shirt. On 6 April 2013, against
Mallorca, he came on as a substitute for Andrés Iniesta in the 50th minute and competed against his brother
Giovani dos Santos.
2013–14 season On 28 August, Dos Santos won the
2013 Supercopa de España with Barça at the Camp Nou.
2014–15 season Dos Santos left Barcelona at the beginning of the
2014–15 season.
Villarreal On 9 July 2014, Dos Santos signed a five-year deal with Villarreal, and going to play with his brother Giovani. On 21 December, Dos Santos scored his first La Liga goal in a 3–0 victory against
Deportivo La Coruña.
Los Angeles Galaxy On 27 July 2017,
MLS club
LA Galaxy announced the signing of Dos Santos as a
Designated Player, reuniting him with his brother,
Giovani, at the American club. Villarreal sold Jonathan for a fee reportedly around €5–6 million. On 29 November 2021, the club parted ways with Dos Santos after his contract expired.
América On 23 December 2021, Dos Santos joined
América on a free transfer. ==International career==