| 1990 | Chansons | Alexander Agricola; Ferrara Ensemble, Crawford Young | | 2 |
| 1992 | Missa Mater Patris / Magnificat and Motets | Josquin, Agricola; Chanticleer | | 1 |
| 1999 | A Secret Labyrinth | Alexander Agricola; Huelgas Ensemble, Paul Van Nevel | | 3 |
| 1999 | Fortuna desperata | Alexander Agricola; Ensemble Unicorn, Michael Posch | | 1 |
| 2001 | Missa Malheur me bat / Missa In minen sin | Alexander Agricola; A:N:S Chorus, János Bali | 4 | 1 |
| 2004 | Missa Le serviteur / Missa Je ne demande | Agricola; A:N:S Chorus, János Bali | 4 | 1 |
| 2006 | Chansons | Alexander Agricola; Fretwork, Michael Chance | | 1 |
| 2010 | Missa in Myne Zyn | Alexander Agricola; Capilla Flamenca, Dirk Snellings | | 1 |
| 2024 | Scaramella | Obrecht, Fitch, Brumel, Agricola; The Binchois Consort, Andrew Kirkman | | 1 |
| 2025 | Masses | Alexander Agricola; Beauty Farm | | 1 |