The draw for this round took place on 9 August 2019. The majority of fixtures were held on 24, 25 and 28 August 2019. Two of the fixtures, Kalamata–Atromitos Patras and Enosis Vathyllos-Pansamiakos–Aiolikos were postponed in light of Kalamata and Aiolikos' bids to enter the Football League. Kalamata were eventually greenlighted to play in the Football League by decision of the HFF, taking the place of Nestos Chrysoupoli, who withdrew its participation. As such, despite being drawn against Atromitos Patras, they advanced to the Third Round draw on walkover. Likewise, Atromitos advanced to the next round on walkover.
Second Round
The draw for this round took place on 27 August 2018.
Third Round
The draw for this round took place on 9 September 2019. A total of 24 teams are involved in the Round 3 draw: The 12 2019−20 Football League teams entering in this round, and the twelve winners of the previous round. 12 single-match fixtures were determined, of which the winners will qualify to the next Round. The majority of fixtures will be held on 14, 15 and 18 September. As a result of the draw, Kalamata advanced to the next round on walkover.
Fourth Round
The draw for this round took place on 17 September 2019. A total of 24 teams are involved in the Round 4 draw: The 12 2019−20 Super League 2 teams entering in this round, and the twelve winners of the previous round. 12 single-match fixtures were determined, of which the winners will qualify to the next Round. The majority of fixtures will be held on 24, 25 and 26 September. As a result of the draw, Panserraikos advanced to the next round on walkover.
Fifth Round
The draw for this round took place on 16 October 2019. A total of 22 teams are involved in the Round 5 draw: The 8 2019−20 Super League teams, who finished in places 6–13 in the 2018−19 season entering the competition in this round, the twelve winners of the previous round, the champion of the 2018–19 Football League, and the single club advancing on walkover in Round 4. As of this phase onward, teams play against each other over two legs on a home-and-away basis, except for the one-match final. In the draw for Round 5, the nine Super League teams are seeded, and the 13 clubs advancing from previous Rounds are unseeded. The seeded teams are drawn against the unseeded teams, with the seeded teams hosting the second leg. The remaining 4 unseeded clubs will be drawn against one another with the team being drawn last hosting the second leg. A total of 11 fixtures were determined, of which the winners will qualify to the Round of 16. The first leg matches will be held on 29, 30 and 31 October, while the 2nd leg matches will be held 3, 4 and 5 December 2019.
Seeding
Summary
Tournament
In the Round of 16, the final five participating clubs are introduced to the tournament. As in the Fifth Round, teams play against each other over two legs on a home-and-away basis, with the exception of the one-match final. The mechanism of the draws for each round is as follows:
In the draw for the round of 16, the five Super League clubs finishing in places 1–5 in the previous season are seeded, while the clubs advancing from Round 5 are unseeded. The seeded teams are drawn against the unseeded teams, with the seeded teams hosting the second leg. The remaining 6 unseeded clubs will be drawn against one another with the team being drawn last hosting the second leg.
In the draws for the quarter-finals onwards, there are no seedings.
