One Hundred and three of the one hundred and four teams who participated in the 2006–07 Terceira Divisão, played in this round. Vitória Setúbal B was unable to compete in the domestic cup competition due to the possibility of encountering their senior side in the competition. Queluz also did not participate.
Fifty four of the fifty six teams who participated in the 2006–07 Segunda Divisão, played in this round. Marítimo B was unable to compete in the domestic cup competition due to the possibility of encountering their senior side in the competition. Queluz also did not participate.
For the first round draw, teams were drawn against each other in accordance to their geographical location. The draw was split up into four sections: teams from the north, the center, the south and the Azores region. The draw for the first round took place on 8 August. All first round cup ties were played on 3 September. Due to the odd number of teams involved at this stage of the competition, 1º de Dezembro, Canedo, Cartaxo, Lajense, Macedo de Cavaleiros, Penamacorense and União da Serra progressed to the next round. Vasco da Gama AC were scheduled to play Casa Pia, but forfeited their match due to the club folding at the beginning of the 2006–07 season. The first round of the cup saw teams from the Portuguese Third Division start the competition alongside some teams who registered to participate in the cup from the Portuguese District Leagues.
The draw for the second round took place on 11 September. All second round ties were played on 24 September. Due to the odd number of teams at this stage of the competition, Avanca, Bougadense, Imortal, Louletano, Maria da Fonte, Marítimo Graciosa, Oliveira do Bairro, Paços de Brandão, Paredes and Tourizense progressed to the next round. The second round saw teams from the Portuguese Second Division enter the competition.
The draw for the third round took place on 30 October. The majority of the third round ties were played on 11 November. Due to the odd number of teams in the competition, Casa Pia progressed to the next round due to having no opponent to face at this stage of the competition. The third round saw teams from the Liga de Honra enter the competition.
Home team
Score
Away team
Avanca
Gondomar
Bragança
Imortal
Camacha
Alcobaça
Capelense
Portimonense
Esmoriz
Pontassolense
Joane
Louletano
Juventude Évora
Pampilhosa
Lagoa
União da Serra
Leixões
Ribeirão
Lourosa
Famalicão
Lusitânia
Chaves
Mafra
Vitória de Guimarães
Maia
Madalena
Marco
Lousada
Maria da Fonte
Bougadense
Mirandela
Feirense
Odivelas
Ataense
Olivais e Moscavide
Tocha
Operário
Rio Ave
Penalva do Castelo
1º de Dezembro
Home team
Score
Away team
Pinhalnovense
Paços de Brandão
Rebordosa
Macedo de Cavaleiros
Santa Clara
Beira-Mar de Monte Gordo
Sátão
Olhanense
Sertanense
Barreirense
Sintrense
Estoril
Sourense
Santiago
Sporting da Covilhã
Tourizense
Sporting de Espinho
Eléctrico
Torreense
Atlético CP
Trofense
Rio Maior
União da Madeira
Machico
União de Lamas
Santana
Valdevez
Paredes
Vizela
Oliveira do Bairro
Oliveirense
Ferreiras
AD Oliveirense
Moreirense
Valecambrense
Marítimo Graciosa
Penafiel
Varzim
Leça
Fourth round
The draw for the fourth round took place on 28 November. Sporting CP's cup tie against União da Madeira was played on 21 December, whilst Benfica's tie against Oliveira do Bairro was played on 6 January. The remainder of the ties were played on 7 January. Due to the odd number of teams in the competition, Rio Ave progressed to the next round due to having no opponent to face at this stage of the competition. The fourth round saw teams from the Primeira Liga enter the competition.
Home team
Score
Away team
União da Madeira
Sporting CP
Benfica
Oliveira do Bairro
Porto
Atlético CP
Bragança
Marco
Gondomar
Rio Maior
Leixões
Famalicão
Paredes
Belenenses
Penalva do Castelo
Maria da Fonte
Santiago
Odivelas
Valecambrense
Varzim
Beira-Mar
Santana
Boavista
Macedo de Cavaleiros
Camacha
Olhanense
Desportivo das Aves
Oliveirense
Home team
Score
Away team
Estoril
Santa Clara
Estrela da Amadora
Feirense
Juventude Évora
Pinhalnovense
Louletano
Sporting de Espinho
Maia
Lagoa
Nacional
Vizela
Penafiel
Marítimo
Pontassolense
Olivais e Moscavide
Naval
Casa Pia
Sertanense
Lusitânia
Sporting da Covilhã
Mafra
Académica de Coimbra
Vitória de Setúbal
Braga
Portimonense
Paços de Ferreira
União de Leiria
Fifth round
The draw for the fourth round took place on 9 January. All of the cup ties were played on 21 January. Due to the odd number of participants in the competition, Bragança progressed to the next round due to having no opponent to face at this stage of the competition.
Sixth round
Ties were played on 10 February. Due to the odd number of participants involved in the 2006–07 Taça de Portugal, Braga qualified for the quarter finals due to having no opponent to face at this stage of the competition.
Quarter-finals
Three of the cup ties were played on 28 February, whilst Braga's game against Varzim was played on 25 March.
Semi-finals
Ties were played on 18–19 April. All four semi-finalists were from the Primeira Liga.