Chung was the Paris Opera's music director from 1989 to 1994, during which time he opened the inaugural season of the then-new Opéra Bastille.

In 1991, the Association of French Theatres and Music Critics named him "Artist of the year" and in 1992 he received the Legion d'Honneur for his contribution to the Paris Opéra.

These include Olivier Messiaen's Turangalîla-Symphonie and Éclairs sur l'au-delà…, Verdi's Otello, Berlioz's Symphonie fantastique, and Shostakovich's Lady Macbeth of Mtsensk with the Bastille Opera Orchestra; he has also performed a series of Dvořák's symphonies and serenades with the Vienna Philharmonic Orchestra, a series dedicated to great sacred music with the Orchestra dell'Accademia Nazionale di Santa Cecilia, including an award-winning recording of Duruflé's and Fauré's Requiems with Cecilia Bartoli and Bryn Terfel.

He directed the world premiere of Messiaen's last work: the Concert à quatre for four soloists and orchestra, which the composer had dedicated to Myung-whun Chung and the Orchestre de la Bastille.

[6] During this period the Seoul Philharmonic became the first Asian orchestra to sign a major-label record deal[7] and gave its first performance at The Proms.