Entering the competition, the winners were assured of a place in the group stage of the 2012–13 UEFA Europa League.
Alcalá, Cádiz, Sant Andreu, San Roque Lepe, Albacete, Roquetas, Orihuela and Alavés received a bye.
The draw for the third round was held on 15 September 2011 at 13:00 CEST at the Ciudad del Fútbol de Las Rozas in Madrid.
The draw for the Round of 32 was held on 14 October 2011 at 13:00 CEST in La Ciudad del Fútbol in Las Rozas, Madrid.
The draw for Round of 16, Quarterfinals and Semifinals was held on 23 December 2011 at 10:00 CET in the Ciudad del Fútbol de Las Rozas in Madrid.