In the former capacity, he amassed Segunda División totals of 185 matches and 45 goals over six seasons, also representing Granada 74 and Alicante in the competition.

[1][2] In 2004–05, as his contract expired, Francisco seized the opportunity to make his La Liga debut and signed with Albacete.

[7] After narrowly avoiding relegation in the last matchday, and winning La Liga Manager of the Month for November and May,[8][9] Francisco inked a new one-year deal at the Estadio de los Juegos Mediterráneos on 27 May 2014.

[13] On 28 June 2018, Francisco signed with Córdoba still in the second division,[14] but he resigned on 2 August due to the club's poor financial situation.

[17] Francisco returned to the second division on 30 June 2020, taking over from José Luis Martí at fifth-placed Girona for the last six games of the season and the following campaign.