| Segunda Division | 1 | 2012-08-19 | AWAY | AD Alcorcon | 1-1 |
| Segunda Division | 2 | 2012-08-25 | HOME | Girona FC | 1-5 |
| Segunda Division | 3 | 2012-09-01 | AWAY | Villarreal CF | 2-1 |
| Segunda Division | 4 | 2012-09-08 | HOME | FC Barcelona B | 0-1 |
| Segunda Division | 5 | 2012-09-15 | AWAY | UD Almeria | 4-0 |
| Segunda Division | 6 | 2012-09-22 | HOME | Real Madrid Castilla | 3-4 |
| Segunda Division | 7 | 2012-09-29 | AWAY | CD Sabadell | 2-1 |
| Segunda Division | 8 | 2012-10-06 | HOME | Xerez | 1-1 |
| Segunda Division | 9 | 2012-10-13 | HOME | SD Ponferradina | 2-0 |
| Segunda Division | 10 | 2012-10-20 | AWAY | Hercules Alicante CF | 0-0 |
| Segunda Division | 11 | 2012-10-27 | HOME | Las Palmas | 2-3 |
| Segunda Division | 12 | 2012-11-04 | AWAY | Cordoba | 1-0 |
| Segunda Division | 13 | 2012-11-10 | HOME | Sporting Gijon | 2-1 |
| Segunda Division | 14 | 2012-11-18 | AWAY | SD Huesca | 2-1 |
| Segunda Division | 15 | 2012-11-24 | HOME | Recreativo de Huelva | 1-0 |
| Segunda Division | 16 | 2012-12-02 | AWAY | CD Mirandes | 0-0 |
| Segunda Division | 17 | 2012-12-08 | HOME | Numancia CD | 5-1 |
| Segunda Division | 18 | 2012-12-15 | AWAY | Real Murcia | 0-1 |
| Segunda Division | 19 | 2012-12-22 | HOME | Racing de Santander | 1-1 |
| Segunda Division | 20 | 2013-01-06 | AWAY | CD Lugo | 0-0 |
| Segunda Division | 21 | 2013-01-12 | HOME | FC Elche | 0-0 |
| Segunda Division | 22 | 2013-01-19 | HOME | AD Alcorcon | 3-0 |
| Segunda Division | 23 | 2013-01-26 | AWAY | Girona FC | 2-0 |
| Segunda Division | 24 | 2013-02-02 | HOME | Villarreal CF | 0-0 |
| Segunda Division | 25 | 2013-02-09 | AWAY | FC Barcelona B | 0-1 |
| Segunda Division | 26 | 2013-02-16 | HOME | UD Almeria | 2-2 |
| Segunda Division | 27 | 2013-02-24 | AWAY | Real Madrid Castilla | 2-1 |
| Segunda Division | 28 | 2013-03-03 | HOME | CD Sabadell | 1-1 |
| Segunda Division | 29 | 2013-03-09 | AWAY | Xerez | 0-1 |
| Segunda Division | 30 | 2013-03-17 | AWAY | SD Ponferradina | 2-2 |
| Segunda Division | 31 | 2013-03-24 | HOME | Hercules Alicante CF | 0-2 |
| Segunda Division | 32 | 2013-03-30 | AWAY | Las Palmas | 0-1 |
| Segunda Division | 33 | 2013-04-07 | HOME | Cordoba | 3-1 |
| Segunda Division | 34 | 2013-04-13 | AWAY | Sporting Gijon | 3-0 |
| Segunda Division | 35 | 2013-04-20 | HOME | SD Huesca | 1-0 |
| Segunda Division | 36 | 2013-04-28 | AWAY | Recreativo de Huelva | 1-0 |
| Segunda Division | 37 | 2013-05-04 | HOME | CD Mirandes | 1-1 |
| Segunda Division | 38 | 2013-05-11 | AWAY | Numancia CD | 2-2 |
| Segunda Division | 39 | 2013-05-20 | HOME | Real Murcia | 3-1 |
| Segunda Division | 40 | 2013-05-26 | AWAY | Racing de Santander | 0-0 |
| Segunda Division | 41 | 2013-06-02 | HOME | CD Lugo | 0-1 |
| Segunda Division | 42 | 2013-06-08 | AWAY | FC Elche | 3-1 |
