During his career, he was mainly associated with Betis and Valencia, appearing in a joint-record 622 La Liga matches over 20 seasons and scoring 77 goals while winning the Copa del Rey with both clubs (twice with the former).

In 1999–2000 he started his senior career, appearing regularly for Real Betis B (after spending two years in the youth ranks) as it was eventually relegated from the Segunda División B.

Joaquín was loaned to Albacete Balompié as punishment by Betis owner Manuel Ruiz de Lopera, due to the player taking a certain percentage of the transfer fee.

[9] In late August 2006, Joaquín officially moved to Valencia for €25 million, making him the club's most expensive signing to that date as the player penned a five-year contract, with the choice of a further one-year extension.

[15] He made his debut for the club on 28 August in a 2–1 away loss against Sevilla FC,[16] and opened his scoring account by netting twice in another local derby, a 4–0 home defeat of Granada CF.

[17] In two home games in October 2012 separated by only four days, Joaquín scored to give his team the final win, on both occasions after having missed a penalty: he started against Real Valladolid (2–1),[18] then netted the match's only against AC Milan in the Champions League group stage.

[20] He made his competitive debut for his new team on 29 August, starting in a 1–0 home loss against Grasshopper Club Zürich in the Europa League playoff round.

[21] Joaquín's first goal for the Viola came as a substitute on 20 October 2013, in a 4–2 home win over Serie A champions Juventus FC,[22] and his second of the league season was the only one in a victory at SSC Napoli the following 23 March.

[32] On 16 July 2020, in a 2–1 home loss to Deportivo Alavés, Joaquín made his 551st Spanish top-division appearance, thereby surpassing Raúl as the outfield player with the most games in the competition; only goalkeeper Andoni Zubizarreta remained ahead of him, on 622.

[33] On 15 September 2022, after scoring in the 3–2 defeat of PFC Ludogorets Razgrad in the group stage, he became the oldest player to achieve the feat in the history of the Europa League at 41 years and 56 days.

[39] Brilliant club form for Betis saw him get called up for that year's FIFA World Cup, where he appeared twice: in his second match, the quarter-finals against co-hosts South Korea, he was involved in a couple of debatable decisions, including one incident where the linesman raised his flag for a goal kick as Joaquín was crossing a ball to Fernando Morientes, who was denied a golden goal – the argument was that the ball had crossed the line.

He later commented, "The only thing I wanted to say is that these are not clear times for the national squad after losing to Northern Ireland .... but it was not my intention to attack the team or Luis Aragonés".

[45] In October 2022, after a long and successful presence on television and social media, he made his debut as a TV host in prime time, with El novato, an interview program with popular personalities with a wide audience since its inception.