Similar to the previous tournament, the Smart National Club championships this year had cluster and regional eliminations outside of Manila and the quarterfinal matches were hosted in the provinces.
[5] Member Associations (MA) of the Philippine Football Federation organized their own tournaments as part of Provincial Qualifying Rounds to determine their representatives to the group stages.
[6] 1 Competing as a guest club in the UFL; General Trias International FC is a member of Cavite Football Association.
2 Competing as a Division 1 club in the UFL; Stallion is a member of Iloilo Football Association.
North, Central and South Luzon cluster eliminations were held in La Trinidad, Benguet on October 17, 2012.
[13] Mindanao hosted the most number of cluster elimination rounds, taking place in Malaybalay on 17 October 2012 while South Cotabato and Dipolog commenced thereafter.
Games were played in single round-robin format where winners and runners-up advanced to the next round.
[7] Winners and runners-up from both Luzon clusters will advance to the All-Luzon Championship and will compete in single-round robin format.
[7] Winners from the four Mindanao clusters will advance to the All-Mindanao Championship and will compete in single-round robin format.