Gaubert was named musical director of the Paris Opéra in 1920 and ultimately began to teach at the École Normale de Musique. Although Gaubert practiced the flute for a half hour before each lesson given until the end of his teaching career, the demands of his various commitments impacted his flute technique and he ceded his flute teaching position at the Conservatoire to Marcel Moyse. In 1930, however, Vincent d'Indy yielded his own post as leader of the conducting class to Gaubert, who kept it until passing the baton to Charles Münch in 1938. Gaubert was still conducting with the Opéra when it was evacuated to his hometown of Cahors in June 1940, it returned to Paris at the end of the summer. Gaubert remained unflappable and optimistic even in the face of the Second World War, but died, suddenly, of a stroke just hours before he was to take the podium to lead the premiere of his ballet Le chevalier et la demoiselle.
Gaubert was a weekend composer who wrote, among his 80 or so works, several pieces for flute that have become an important part of the flute repertoire. Despite his prominence as a conductor and soloist and having left a generous bequest of recordings as conductor, it is his compositions for which Gaubert is best known in posterity. They are graciously written, fully idiomatic for the flute, and demonstrate a grasp of French impressionist harmonic language even though they tend to lack sophistication in formal development and, to some degree, taste.