Nagano also revitalised the Hallé Orchestra's profile both with major tours and recordings.

Following a Japanese tour in 1996, Nagano took the Hallé to the Salzburg Festival for a revival of Peter Sellars' production of Messiaen's epic operatic meditation Saint François d'Assise which, in 1998, was recorded live for Deutsche Grammophon's 20/21 label.

For Erato, Nagano conducted the Hallé in a number of world première recordings, including three Britten works.  The original four-act Billy Budd was recorded live, with Thomas Hampson as Budd and Anthony Rolfe Johnson as Captain Vere (1998).  Gidon Kremer and Yuri Bashmet performed the première of the recently rediscovered Double Concerto for violin and viola (1999), after the radio oratorio The Rescue of Penelope, a similar find, was also released (1996).

Also for Erato Nagano recorded the newly issued critical edition of Mahler's early Das klagende Lied in its original three-part form (1998), while for Teldec a recent release has been songs from Des Knaben Wunderhorn, Kindertotenlieder and Rückertlieder with a long-time Nagano artistic collaborator, Dietrich Henschel.