Nelsons topped the Orchestral music category for his recording of Shostakovich’s Symphony No 10 for Deutsche Gramophon with the Boston Symphony Orchestra.
The same recording won a Grammy Award in February.
Nelsons also won a Contemporary Award for his recording of Hans Abrahamsen’s Let Me Tell You, a work based on Shakespeare’s Ophelia to a libretto by Paul Griffiths. In the recording, Nelsons conducted the Bavarian Radio Symphony Orchestra with soprano Barbara Hannigan.
The award winners are picked by music critics and a number of retailers, broadcasters, administrators, and performers. The Gramophone awards are among the most sought-after in the world of classical music.
The awards will be presented on September 15 at London's St John's, Smith Square where the winner of the the Gramophone Recording of the Year award will be announced as well.
The ceremony will be streamed on the Medici.TV website.