| Ensemble Modern Plays Frank Zappa: Greggery Peccary & Other Persuasions | Frank Zappa; Ensemble Modern, Jonathan Stockhammer | CD | 10 | | RCA Red Seal | 82876 56061 2 | 828765606127 |
| Ensemble Modern Plays Frank Zappa: Greggery Peccary & Other Persuasions | Frank Zappa; Ensemble Modern, Jonathan Stockhammer | CD | 10 | | RCA Red Seal | BVCC-31075 | |
| Ensemble Modern Plays Frank Zappa: Greggery Peccary & Other Persuasions | Frank Zappa; Ensemble Modern, Jonathan Stockhammer | CD | 10 | | RCA Red Seal | | 828765984225 |
| Battleship Potemkin | Tennant/Lowe; Pet Shop Boys, Dresdner Sinfoniker, Jonathan Stockhammer | CD | 15 | | Parlophone | 8744502 | 0724387445024 |
| Battleship Potemkin | Tennant/Lowe; Pet Shop Boys, Dresdner Sinfoniker, Jonathan Stockhammer | Copy Control CD | 15 | | Gala Records , Parlophone | 0946348306 2 1 | 094634830621 |
| 1. Symphonie / 2. Symphonie / Nachtwach / Vers une symphonie fleuve III / Raumauge | Wolfgang Rihm; Radio‐Sinfonieorchester Stuttgart des SWR, Jonathan Stockhammer, Gianluigi Gelmetti, SWR Vokalensemble Stuttgart, Marcus Creed, Rupert Huber | Digital Media | 7 | | Hänssler Classic | | |
| 1. Symphonie / 2. Symphonie / Nachtwach / Vers une symphonie fleuve III / Raumauge | Wolfgang Rihm; Radio‐Sinfonieorchester Stuttgart des SWR, Jonathan Stockhammer, Gianluigi Gelmetti, SWR Vokalensemble Stuttgart, Marcus Creed, Rupert Huber | CD | 7 | | Hänssler Classic | CD-No. 93.227 | 4010276020592 |
| Ensemble Modern Plays Frank Zappa: Greggery Peccary & Other Persuasions | Frank Zappa; Ensemble Modern, Jonathan Stockhammer | Digital Media | 11 | | RCA Red Seal | | [none] |
| Symphonie Du Jaguar / Vague De Pierre | Thierry Pécou; Ensemble Zellig, Orchestre philharmonique de Radio France, Jonathan Stockhammer, François‐Xavier Roth | CD | 8 | | Harmonia Mundi | HMC905267 | 794881941223 |
| Hans Abrahamsen: Zählen und erzählen | Jonathan Stockhammer | Digital Media | 18 | | Winter & Winter | | |
| Les Liaisons magnétiques | Thierry Pécou; Ensemble Variances, Ensemble Resonanz, Jonathan Stockhammer | CD | 8 | | æon | AECD 1546 | 3760058360460 |
| Symphony No. 3 Op. 96 | Hugo Kaun ; Jonathan Stockhammer, Rundfunk‐Sinfonieorchester Berlin | CD | 6 | | Classic Produktion Osnabrück | 555572-2 | 761203557226 |
