The competition format for the 2012–13 edition consists of three rounds plus a knockout phase. In the first round, only teams competing in the 2012–13 Segunda Liga (excluding reserve teams from Primeira Liga clubs) take part. The sixteen teams are drawn into four groups of four teams, where each team plays against the other three in a single round-robin format. The group winners and runners-up advance to the second round.
In the second round, the eight teams that qualified from the previous round are joined by the six Primeira Liga teams placed 9th to 14th in the previous season and the two teams promoted to 2012–13 Primeira Liga. Two-legged home-and-away fixtures are played between Segunda Liga teams qualifying from the first round and Primeira Liga teams entering this round, and the winner advances to the third round.
The third round features the eight winners of the previous round the remaining eight Primeira Liga teams, ranked 1st to 8th in the previous season. Similarly to the first round, the sixteen teams are drawn into four groups of four teams, according to a seeding based on their classification in the previous season. Each team plays against the other three in a single round-robin format, and only the group winners advance to the knockout phase. The knockout phase consists of semi-finals and one final, both decided in one-legged fixtures. The final match is played at a neutral venue.
The 32 teams competing in the two professional tiers of Portuguese football for the 2012–13 season are eligible to participate in this competition. For Primeira Liga teams, the final league position in the previous season determines if they enter in the second or third round of the Taça da Liga.
Sporting da Covilhã finished 15th in the 2011–12 Segunda Liga, in position to be relegated to the Second Division for the 2012–13 season. However, as União de Leiria – which were relegated from the Primeira Liga, together with Feirense – were unable to fulfill the LPFP requirements mandatory for entry in professional competitions, they were further relegated to the Second Division and Covilhã was invited to take União de Leiria's place.
Portimonense finished 16th (last) in the 2011–12 Segunda Liga, in position to be relegated to the Second Division for the 2012–13 season. However, as 2011–12 Second Division champions Varzim were unable to fulfill the LPFP requirements mandatory for entry in professional competitions, they were not promoted to the Segunda Liga, together with Tondela, and so Portimonense were invited to take Varzim's place.