The former B team head coach kept the Spanish club in La Liga last season after taking charge at the start of the 2013-14 campaign.
However, Monday's 5-2 defeat at Eibar proved the final straw, with Almeria taking just two points from their last eight league matches.
Francisco, 36, recently became the club's longest-serving manager in La Liga, surpassing Unai Emery's previous record.
Almeria currently sit 17th in the La Liga table.
Restore Data
| Team | P | W | D | L | F | A | GD | PTS | |
| 1 | Huesca | 8 | 5 | 0 | 3 | 13 | 7 | 6 | 15 |
| 2 | Levante | 7 | 4 | 2 | 1 | 14 | 9 | 5 | 14 |
| 3 | Racing de SantanderRacing | 7 | 4 | 2 | 1 | 11 | 7 | 4 | 14 |
| 4 | Burgos | 7 | 4 | 2 | 1 | 11 | 7 | 4 | 14 |
| 5 | Real ZaragozaZaragoza | 7 | 4 | 1 | 2 | 11 | 4 | 7 | 13 |
| 6 | MirandesMirandes | 7 | 3 | 3 | 1 | 5 | 2 | 3 | 12 |
| 7 | EibarEibar | 7 | 3 | 3 | 1 | 9 | 7 | 2 | 12 |
| 8 | Eldense | 7 | 3 | 2 | 2 | 8 | 8 | 0 | 11 |
| 9 | Real Oviedo | 7 | 3 | 2 | 2 | 6 | 7 | -1 | 11 |
| 10 | CastellonCastellon | 7 | 3 | 1 | 3 | 10 | 8 | 2 | 10 |
| 11 | ElcheElche | 7 | 3 | 1 | 3 | 9 | 8 | 1 | 10 |
| 12 | Malaga | 7 | 2 | 4 | 1 | 8 | 9 | -1 | 10 |
| 13 | Sporting GijonSporting Gijon | 7 | 2 | 3 | 2 | 7 | 6 | 1 | 9 |
| 14 | Albacete | 7 | 3 | 0 | 4 | 10 | 12 | -2 | 9 |
| 15 | CadizCadiz | 8 | 2 | 3 | 3 | 10 | 14 | -4 | 9 |
| 16 | CordobaCordoba | 7 | 2 | 2 | 3 | 9 | 11 | -2 | 8 |
| 17 | Granada | 7 | 1 | 4 | 2 | 10 | 12 | -2 | 7 |
| 18 | Deportivo La CorunaDeportivo | 7 | 2 | 1 | 4 | 8 | 10 | -2 | 7 |
| 19 | CartagenaCartagena | 7 | 2 | 0 | 5 | 7 | 11 | -4 | 6 |
| 20 | Almeria | 7 | 1 | 3 | 3 | 10 | 15 | -5 | 6 |
| 21 | Racing Club de FerrolRacing de Ferrol | 7 | 0 | 3 | 4 | 4 | 11 | -7 | 3 |
| 22 | TenerifeTenerife | 7 | 0 | 2 | 5 | 5 | 10 | -5 | 2 |
| > Segunda Division Full Table | |||||||||
