| 6 | Roberto Soldado | Group Stage | UEFA Champions League 10/11 |
| 6 | Fernando Morientes | Group Stage | UEFA Champions League 06/07 |
| 5 | Jonas Goncalves | Group Stage | UEFA Champions League 12/13 |
| 5 | Roberto Soldado | Group Stage | UEFA Champions League 11/12 |
| 5 | John Carew | First Group Stage | UEFA Champions League 02/03 |
| 5 | Claudio Lopez | Semi-finals | UEFA Champions League 99/00 |
| 5 | Gaizka Mendieta | Semi-finals | UEFA Champions League 99/00 |
| 5 | Juan Sanchez | First Group Stage | UEFA Champions League 00/01 |
| 4 | Roberto Soldado | Group Stage | UEFA Champions League 12/13 |
| 4 | David Villa | Group Stage | UEFA Champions League 06/07 |
| 4 | Ruben Baraja | First Group Stage | UEFA Champions League 02/03 |
| 4 | Gerard | Quarter-finals | UEFA Champions League 99/00 |
| 4 | Kily Gonzalez | Second Group Stage | UEFA Champions League 99/00 |
| 4 | Diego Alonso | First Group Stage | UEFA Champions League 00/01 |
| 3 | Sofiane Feghouli | Group Stage | UEFA Champions League 12/13 |
| 3 | Jonas Goncalves | Group Stage | UEFA Champions League 11/12 |
| 3 | Tino Costa | Group Stage | UEFA Champions League 10/11 |
| 3 | Juan Sanchez | First Group Stage | UEFA Champions League 02/03 |
| 3 | Pablo Aimar | First Group Stage | UEFA Champions League 02/03 |
| 3 | Adrian Ilie | Second Group Stage | UEFA Champions League 99/00 |
| 3 | Miguel Angel Angulo | Semi-finals | UEFA Champions League 99/00 |
| 3 | John Carew | Second Group Stage | UEFA Champions League 00/01 |
| 2 | Denis Cherychev | Group Stage | UEFA Champions League 19/20 |
| 2 | Kevin Gameiro | Round of 16 | UEFA Champions League 19/20 |
| 2 | Rodrigo Moreno | Group Stage | UEFA Champions League 19/20 |
| 2 | Ferran Torres | Group Stage | UEFA Champions League 19/20 |
| 2 | Santi Mina | Group Stage | UEFA Champions League 18/19 |
| 2 | Sofiane Feghouli | Group Stage | UEFA Champions League 15/16 |
| 2 | Pablo Hernandez | Group Stage | UEFA Champions League 10/11 |
| 2 | Aritz Aduriz | Group Stage | UEFA Champions League 10/11 |
| 2 | David Villa | Group Stage | UEFA Champions League 07/08 |
| 2 | David Silva | Round of 16 | UEFA Champions League 06/07 |
| 2 | Miguel Angel Angulo | Group Stage | UEFA Champions League 06/07 |
| 2 | Vicente | Group Stage | UEFA Champions League 04/05 |
| 2 | Miguel Angel Angulo | First Group Stage | UEFA Champions League 02/03 |
| 2 | Fabio Aurelio | First Group Stage | UEFA Champions League 02/03 |
| 2 | Mista | First Group Stage | UEFA Champions League 02/03 |
| 2 | Ruben Baraja | First Group Stage | UEFA Champions League 00/01 |
| 2 | Gaizka Mendieta | Semi-finals | UEFA Champions League 00/01 |
| 2 | Kily Gonzalez | First Group Stage | UEFA Champions League 00/01 |
| 2 | Roberto Ayala | Second Group Stage | UEFA Champions League 00/01 |
| 1 | Daniel Wass | Group Stage | UEFA Champions League 19/20 |
| 1 | Daniel Parejo | Group Stage | UEFA Champions League 19/20 |
| 1 | Carlos Soler | Group Stage | UEFA Champions League 19/20 |
| 1 | Geoffrey Kondogbia | Group Stage | UEFA Champions League 19/20 |
| 1 | Michy Batshuayi | Group Stage | UEFA Champions League 18/19 |
| 1 | Carlos Soler | Group Stage | UEFA Champions League 18/19 |
| 1 | Andre Gomes | Group Stage | UEFA Champions League 15/16 |
| 1 | Nelson Haedo-Valdez | Group Stage | UEFA Champions League 12/13 |
| 1 | Adil Rami | Round of 16 | UEFA Champions League 12/13 |
| 1 | Tino Costa | Group Stage | UEFA Champions League 11/12 |
| 1 | Adil Rami | Group Stage | UEFA Champions League 11/12 |
| 1 | Pablo Hernandez | Group Stage | UEFA Champions League 11/12 |
| 1 | Aritz Aduriz | Group Stage | UEFA Champions League 11/12 |
| 1 | Joaquin | Group Stage | UEFA Champions League 10/11 |
| 1 | Alejandro Dominguez | Group Stage | UEFA Champions League 10/11 |
| 1 | Juan Mata | Group Stage | UEFA Champions League 10/11 |
| 1 | Roberto Ayala | Group Stage | UEFA Champions League 06/07 |
| 1 | Raul Albiol | Group Stage | UEFA Champions League 06/07 |
| 1 | Bernardo Corradi | Group Stage | UEFA Champions League 04/05 |
