In 1992, music director Claudio Abbado invited him to become principal flutist of the Berlin Philharmonic Orchestra, the same position from which James Galway leapt to international fame. He began accepting international concert performances soon after settling into his position in Berlin. More awards followed, including the Geneva International Music Competition and the European Council's Juventus Prize. His engagements as a concerto soloist, at chamber music festivals, and with his own ensemble Les Vents Français, built to such a point that he resigned his position with the Berlin Philharmonic in late 2000. In the meantime, Pahud had signed with EMI Classics in 1996, beginning a collaboration that greatly expanded the library of recorded flute music. His first EMI disc, released in 1996, was a set of the Mozart Flute Concertos and the Concerto for Flute and Harp. It won the Diapason "CD of the Year" award and the Radio France listeners' poll as favorite recording of the year, among other honors. 2011's Flute Music at Frederick the Great's Court, with Trevor Pinnock, also was an award-winning release.
In 2009, Pahud was honored with the title Chevalier dans l'Ordre des Arts et des Lettres by the French Ministry of Culture.