Koke started his football career at hometown club Málaga CF, being essential as the B team reached the second division for the first time its history, in 2002. On February 23, 2003, he scored a late equalizer in a 1–1 home draw against Celta de Vigo in La Liga, where he appeared in six matches, five from the bench, totalling 176 minutes during the 2002–03 season.
In January 2004, after seeing very little playing time in the first team, Koke joined French league powerhouse Olympique de Marseille, playing ten times without scoring the remainder of the season. The following one was much better, with Koke scoring five in 24 appearances, and making for a pacy attacking trio in Marseille with former French internationals Steve Marlet and Péguy Luyindula.
In 2005–06, with the arrival of Mamadou Niang and Toifilou Maoulida, Koke was deemed surplus to requirements, scoring one goal in nine league games and, in January 2006, was sent on loan to Portugal's Sporting Lisbon, where he played almost no part in the club's season, although he did score twice as a substitute against Gil Vicente, on March 5, in a 2–0 home win.
The arrival (initially on loan) of Djibril Cissé in August 2006 meant the end of Koke's adventure in France. He would eventually sign for Aris Thessaloniki, a team that was filled with Spanish players, in a three-year deal. He produced the best football of his career to date, notching up 10 league goals for a team that finished fourth in the league, after being promoted the previous season.
In 2007–08, Koke scored another 10 in the league's regular season, adding one in the UEFA Cup group stage game against Red Star Belgrade. In July 2008, he signed a new five-year contract with Aris, while also attaining club vice-captaincy, second to Kostas Nebegleras, and becoming himself captain in the 2009–10 campaign.
On August 13, 2008, Koke's girlfriend gave birth to their first daughter, Maria-Ameera. The following day, he dedicated the goal, scored in a UEFA Cup contest against NK Slaven Belupo (1–0 home win), to his newborn.