Reports surfacing on 29 July 2007 indicated that cross-town rivals Atlético Madrid were on the verge of landing Reyes.
Later that day, Wenger confirmed that the player's departure was imminent, and that a more specific announcement would be made shortly.
The following day, he passed his medical and penned a four-year deal reportedly worth €12 million, scoring and assisting once on his debut for a 3–1 defeat of S.S. Lazio in the annual Amsterdam Tournament (while at Arsenal, he was named the tournament's MVP in its 2004 edition); his first campaign with the Colchoneros was disastrous, as he was often kept out of the side by Maxi Rodríguez and Simão Sabrosa and failed to score a single goal in 26 league appearances.

On 7 August 2008, S.L. Benfica announced the signing of Reyes on a one-year loan – the Portuguese also bought 25% of his playing rights for a fee of €2.65 million, and ensured a buying option of the remainder 75% for an undisclosed fee.
His first goal for the Lisbon club was scored against city rivals Sporting CP, on 27 September: after an understanding between Reyes and Pablo Aimar and a pass from the same, he scored in fashion.
Later in the same week he found the net again, against S.S.C. Napoli, helping to a 2–0 home victory in the first round of the UEFA Cup.

Reyes' return to Atlético proved to be much more successful, as he re-united with Quique Sánchez Flores, his manager at Benfica from the previous season.
He scored his first official goal in Spain in more than two years on 9 January 2010, with a long-range effort at Real Valladolid, in a 4–0 win– by then, he had beaten the competition of Maxi and started in the wings alongside Simão.
On 14 February 2010 he put in a Player of the match performance in Atlético's 2–1 victory against FC Barcelona, setting up the opening goal for Diego Forlán in the eventual champions' only league defeat of the season.
Four days later, in the Europa League 1–1 home draw to Galatasaray SK, he scored a stunning free kick from the right wing on the 22nd minute, after he was brought down just outside the box (3–2 aggregate win); on 28 March, he curled in a left-footed shot from the right wing just inside the box, opening the score in the Madrid derby against his former team in an eventual 2–3 loss.

On 27 August 2010, Reyes opened the scoring in the 2–0 defeat of Inter Milan for the UEFA Super Cup, after a one-two combination with Argentine Sergio Agüero.
His first league goal of the campaign came in a 1–4 defeat at Hércules CF on 10 January 2011, which inspired an impressive run of scoring form, with goals in successive home games in February/March, against Valencia CF, former club Sevilla and Villarreal.

Reyes took up more responsibility for 2011–12, and established himself as one of the team's most important players.
On 28 July 2011, he scored twice for Atlético in a 2–1 Europa League win against Strømsgodset IF.
A week later, in the second leg, he was again on the scoresheet and also got an assist for Adrián López in a 2–0 away victory; he struggled to find the consistency he had under Flores and, following a fallout with new coach Gregorio Manzano after being substituted in a 0–3 defeat at Athletic Bilbao, his playing time became more and more limited.
Reports surfacing on 29 July 2007 indicated that cross-town rivals Atlético Madrid were on the verge of landing Reyes. Later that day, Wenger confirmed that the player's departure was imminent, and that a more specific announcement would be made shortly. The following day, he passed his medical and penned a four-year deal reportedly worth €12 million, scoring and assisting once on his debut for a 3–1 defeat of S.S. Lazio in the annual Amsterdam Tournament (while at Arsenal, he was named the tournament's MVP in its 2004 edition); his first campaign with the Colchoneros was disastrous, as he was often kept out of the side by Maxi Rodríguez and Simão Sabrosa and failed to score a single goal in 26 league appearances.
On 7 August 2008, S.L. Benfica announced the signing of Reyes on a one-year loan – the Portuguese also bought 25% of his playing rights for a fee of €2.65 million, and ensured a buying option of the remainder 75% for an undisclosed fee. His first goal for the Lisbon club was scored against city rivals Sporting CP, on 27 September: after an understanding between Reyes and Pablo Aimar and a pass from the same, he scored in fashion. Later in the same week he found the net again, against S.S.C. Napoli, helping to a 2–0 home victory in the first round of the UEFA Cup.
Reyes' return to Atlético proved to be much more successful, as he re-united with Quique Sánchez Flores, his manager at Benfica from the previous season. He scored his first official goal in Spain in more than two years on 9 January 2010, with a long-range effort at Real Valladolid, in a 4–0 win– by then, he had beaten the competition of Maxi and started in the wings alongside Simão. On 14 February 2010 he put in a Player of the match performance in Atlético's 2–1 victory against FC Barcelona, setting up the opening goal for Diego Forlán in the eventual champions' only league defeat of the season. Four days later, in the Europa League 1–1 home draw to Galatasaray SK, he scored a stunning free kick from the right wing on the 22nd minute, after he was brought down just outside the box (3–2 aggregate win); on 28 March, he curled in a left-footed shot from the right wing just inside the box, opening the score in the Madrid derby against his former team in an eventual 2–3 loss.
On 27 August 2010, Reyes opened the scoring in the 2–0 defeat of Inter Milan for the UEFA Super Cup, after a one-two combination with Argentine Sergio Agüero. His first league goal of the campaign came in a 1–4 defeat at Hércules CF on 10 January 2011, which inspired an impressive run of scoring form, with goals in successive home games in February/March, against Valencia CF, former club Sevilla and Villarreal.
Reyes took up more responsibility for 2011–12, and established himself as one of the team's most important players. On 28 July 2011, he scored twice for Atlético in a 2–1 Europa League win against Strømsgodset IF. A week later, in the second leg, he was again on the scoresheet and also got an assist for Adrián López in a 2–0 away victory; he struggled to find the consistency he had under Flores and, following a fallout with new coach Gregorio Manzano after being substituted in a 0–3 defeat at Athletic Bilbao, his playing time became more and more limited.
José Antonio Reyes