| 1999 | Piano Quintet, etc. | Kapustin | | 1 |
| 2000 | Piano Music | Nikolai Kapustin; Steven Osborne | | 1 |
| 2000 | Kapustin Plays Kapustin: 24 Preludes | Nikolai Kapustin | | 4 |
| 2000 | Kapustin Plays Kapustin: 8 Concert Etudes | Nikolai Kapustin | | 4 |
| 2004 | Piano Music | Nikolai Kapustin; Marc-André Hamelin | | 1 |
| 2004 | 24 Preludes and Fugues for Piano, op. 82 / Violin Sonata | Kapustin | | 1 |
| 2004 | Last Recording | Nikolai Kapustin | | 2 |
| 2005 | Piano Works 2 | Kapustin; Masahiro Kawakami | | 1 |
| 2005 | Piano Works 1 | Kapustin; Masahiro Kawakami | | 1 |
| 2008 | Piano Sonata no. 15 / Preludes / Etudes / Bagatelles | Nikolai Kapustin; John Salmon | | 1 |
| 2008 | Kapustin Returns! | Nikolai Kapustin; Nikolai Kapustin | | 1 |
| 2008 | Piano Works 3 | Kapustin; Masahiro Kawakami | | 1 |
| 2008 | Saxophone Concertos | Kapustin, Eshpai | | 2 |
| 2009 | Shan-shan Sun plays Nikolai Kapustin | Nikolai Kapustin, Lowell Liebermann, Li Yinghai; Shan-shan Sun | | 2 |
| 2011 | Eight Concert Etudes / 24 Preludes in Jazz Style | Nikolai Kapustin; Catherine Gordeladze | | 1 |
| 2014 | Etude | Sergei Lyapunov, Unsuk Chin, Karol Szymanowski, Nikolai Kapustin; Clare Hammond | | 2 |
| 2015 | The Balmoral Recordings 2015 | Fryderyk Chopin, Franz Liszt, Johann Sebastian Bach, Николaй Гиршевич Кaпустин; Aveline Gram | | 1 |
| 2016 | Works for Cello | Nikolai Kapustin; Christine Rauh, Peter Lehel, Benyamin Nuss, Ni Fan, Deutsche Radio Philharmonie Kaiserslautern Saarbrücken, Nicholas Collon | | 1 |
| 2017 | Schumann / Elgar / Kapustin | Schumann, Elgar, Kapustin; Alexander Zagorinsky, Chamber Orchestra of the Vologda Philharmonic Society, Alexander Loskutov | | 2 |
| 2017 | Complete Music for Cello and Piano | Nikolai Kapustin; Duo Perfetto | | 1 |
| 2019 | Complete Chamber Works for Flute | Nikolai Kapustin; Immanuel Davis, Adam Kuenzel, Pitnarry Shin, Käthe Jarka, Timothy Lovelace | | 1 |
| 2020 | Moon Rainbow | Bach, Kapustin; Luisa Imorde | | 2 |
| 2020 | Transitions: Cello Concertos | Kapustin, Schnittke; Eckart Runge, Rundfunk‐Sinfonieorchester Berlin, Frank Strobel | | 1 |
| 2020 | Saxophone Chamber Music | Nikolai Kapustin; Elisaveta Blumina, Peter Bruns, Clair-Obscur Saxophonquartett | | 1 |
| 2021 | Kapustin | Kapustin; Yeol Eum Son | | 1 |
| 2021 | Obsessive Play | Kapustin, Gershwin, Crespo; Daniel Crespo | | 1 |
| 2021 | Piano Concerto no. 4 / Double Concerto / Chamber Symphony | Nikolai Kapustin; Frank Dupree, Rosanne Philippens, Württembergisches Kammerorchester Heilbronn, Case Scaglione | 5 | 2 |
| 2022 | Blueprint | Nikolai Kapustin; Frank Dupree, Jakob Krupp, Meinhard Jenne | | 1 |
| 2022 | New Memories | Nikolai Kapustin, A Bu | | 2 |
| 2022 | Piano Concerto No. 2 / 8 Concert Etudes | Rachmaninov, Kapustin; Nobuyuki Tsujii, Vasily Petrenko, Royal Liverpool Philharmonic Orchestra | | 1 |
| 2023 | Piano Concerto No. 5 / Concerto Op. 104 / Sinfonietta Op. 49 | Nikolai Kapustin; Frank Dupree, Rundfunk‐Sinfonieorchester Berlin, Dominik Beykirch | | 2 |
| 2024 | Piano Concertos Nos. 2 and 6 | Nikolai Kapustin; Frank Dupree, SWR Big Band, SWR Symphonieorchester, Dominik Beykirch | | 1 |
