After a loan stint with neighbours Villarreal CF he was sold to Albacete Balompié, making his La Liga debut on 8 January 1995 in a 1–0 home win against Real Oviedo.

[4] Joining 2000 league champions Deportivo La Coruña after Atlético's relegation, Molina helped win a Spanish cup and two supercups, being an undisputed starter throughout his stint in Galicia.

However, on 14 October 2002, he announced that he suffered from testicular cancer,[5][6] and that he was forced to undergo treatment for his illness, thus missing most of the 2002–03 campaign (ten league appearances, as Depor finished third); he eventually recovered fully.

[7][8] After his link expired,[9] Molina returned home to Valencia for 2006–07, playing for top-division strugglers Levante UD, but did not renew his contract after the season's end, retiring subsequently after the club retained its league status.

[24] In July 2018, Molina was appointed as sporting director of the Royal Spanish Football Federation, replacing Fernando Hierro who had resigned in the aftermath of Spain's performance at the 2018 FIFA World Cup.