| 5 | Roberto Ayala | Group Stage | UEFA Champions League 06/07 |
| 5 | David Albelda | Group Stage | UEFA Champions League 06/07 |
| 5 | Gaizka Mendieta | First Group Stage | UEFA Champions League 00/01 |
| 5 | Ruben Baraja | First Group Stage | UEFA Champions League 00/01 |
| 5 | Amedeo Carboni | First Group Stage | UEFA Champions League 00/01 |
| 4 | Roberto Soldado | Group Stage | UEFA Champions League 12/13 |
| 4 | Ruben Baraja | First Group Stage | UEFA Champions League 02/03 |
| 4 | Gerard | Quarter-finals | UEFA Champions League 99/00 |
| 4 | Claudio Lopez | Semi-finals | UEFA Champions League 99/00 |
| 4 | Mauricio Pellegrino | First Group Stage | UEFA Champions League 00/01 |
| 3 | Ezequiel Garay | Group Stage | UEFA Champions League 19/20 |
| 3 | Daniel Wass | Group Stage | UEFA Champions League 19/20 |
| 3 | Jose Gaya | Group Stage | UEFA Champions League 18/19 |
| 3 | Shkodran Mustafi | Group Stage | UEFA Champions League 15/16 |
| 3 | David Albelda | Group Stage | UEFA Champions League 10/11 |
| 3 | Carlos Marchena | Group Stage | UEFA Champions League 04/05 |
| 3 | Mauricio Pellegrino | First Group Stage | UEFA Champions League 02/03 |
| 3 | Mista | First Group Stage | UEFA Champions League 02/03 |
| 3 | Mauricio Pellegrino | Final | UEFA Champions League 99/00 |
| 3 | Amedeo Carboni | Semi-finals | UEFA Champions League 99/00 |
| 3 | Javier Farinos | Final | UEFA Champions League 99/00 |
| 3 | Kily Gonzalez | First Group Stage | UEFA Champions League 00/01 |
| 3 | Miguel Angel Angulo | First Group Stage | UEFA Champions League 00/01 |
| 3 | Roberto Ayala | Second Group Stage | UEFA Champions League 00/01 |
| 2 | Gabriel Paulista | Group Stage | UEFA Champions League 19/20 |
| 2 | Francis Coquelin | Group Stage | UEFA Champions League 19/20 |
| 2 | Mouctar Diakhaby | Group Stage | UEFA Champions League 19/20 |
| 2 | Daniel Parejo | Group Stage | UEFA Champions League 18/19 |
| 2 | Carlos Soler | Group Stage | UEFA Champions League 18/19 |
| 2 | Geoffrey Kondogbia | Group Stage | UEFA Champions League 18/19 |
| 2 | Andre Gomes | Group Stage | UEFA Champions League 15/16 |
| 2 | Santi Mina | Group Stage | UEFA Champions League 15/16 |
| 2 | Enzo Perez | Group Stage | UEFA Champions League 15/16 |
| 2 | David Albelda | Group Stage | UEFA Champions League 12/13 |
| 2 | Antonio Barragan | Group Stage | UEFA Champions League 12/13 |
| 2 | Vicente Guaita | Group Stage | UEFA Champions League 12/13 |
| 2 | Tino Costa | Group Stage | UEFA Champions League 12/13 |
| 2 | Victor Ruiz | Group Stage | UEFA Champions League 11/12 |
| 2 | David Albelda | Group Stage | UEFA Champions League 11/12 |
| 2 | Ever Banega | Group Stage | UEFA Champions League 11/12 |
| 2 | Tino Costa | Group Stage | UEFA Champions League 11/12 |
| 2 | Aritz Aduriz | Group Stage | UEFA Champions League 10/11 |
| 2 | Juan Mata | Group Stage | UEFA Champions League 10/11 |
| 2 | Carlos Marchena | Group Stage | UEFA Champions League 07/08 |
| 2 | Miguel Angel Angulo | Group Stage | UEFA Champions League 06/07 |
| 2 | Miguel Angel Angulo | Group Stage | UEFA Champions League 04/05 |
| 2 | Bernardo Corradi | Group Stage | UEFA Champions League 04/05 |
| 2 | Ruben Baraja | Group Stage | UEFA Champions League 04/05 |
| 2 | David Albelda | First Group Stage | UEFA Champions League 02/03 |
| 2 | Francisco Rufete | Second Group Stage | UEFA Champions League 02/03 |
| 2 | Santiago Canizares | Second Group Stage | UEFA Champions League 02/03 |
| 2 | Pablo Aimar | Second Group Stage | UEFA Champions League 02/03 |
| 2 | Roberto Ayala | First Group Stage | UEFA Champions League 02/03 |
| 2 | Kily Gonzalez | Second Group Stage | UEFA Champions League 02/03 |
| 2 | David Albelda | Second Group Stage | UEFA Champions League 99/00 |
| 2 | Gaizka Mendieta | Second Group Stage | UEFA Champions League 99/00 |
| 2 | Kily Gonzalez | Quarter-finals | UEFA Champions League 99/00 |
| 2 | Santiago Canizares | Final | UEFA Champions League 99/00 |
| 2 | Miroslav Djukic | Second Group Stage | UEFA Champions League 99/00 |
| 2 | David Albelda | First Group Stage | UEFA Champions League 00/01 |
