^1 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.
^2 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.[6] All first round cup ties were played on 3 September.[7][8] 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.[9] 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.[10] The first round of the cup saw teams from the Terceira Divisão (IV) start the competition alongside some teams who registered to participate in the cup from the Portuguese District Leagues (V).
The draw for the third round took place on 30 October.[14] The majority of the third round ties were played on 11 November.[15][16] 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 (II) enter the competition.
The draw for the fourth round took place on 28 November.[17]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.[18][19] The remainder of the ties were played on 7 January.[20][21] 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 (I) enter the competition.
The draw for the fourth round took place on 9 January.[22] All of the cup ties were played on 21 January.[23][24] 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.
Ties were played on 10 February.[25][26] 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.[27]