Cartagena and Cádiz played off to decide who were the second division B champions. Cádiz won 3-2 on aggregate. (06.06.09)
| 6 Jun | Cádiz Rubiato |
1-1 | Cartagena Armando |
The two losers from the ties between group champions, Real Unión and Alcoyano, have been joined by the six winners from the other knock-out games in the play-off semi-finals. The four winners go in to a new draw on 8th June for the final play-off pairings for the two promotion remaining spots. Second leg results were follows (teams through to the next round in bold):
| 6 Jun | Real Unión Goikoetxea (Pen) |
1-1 | Sabadell Jaume |
| 7 Jun | Alcoyano Rafa Gómez, Patri |
2-1 | Alcorcón Cristian |
| 7 Jun | Jaén Arriaga |
1-0 | Ponferradina |
| 7 Jun | Lorca Manu Busto (2, 1 Pen) |
2-3 | Villarreal B Cristóbal (2), Joan Tomás (Pen) |