Taffanel built a substantial career as both soloist and orchestral player over 30 years, becoming known as the foremost flautist of his time and reestablishing the instrument in the mainstream of music.
As Professor, he revised the institute's repertoire and teaching methods, restructuring the traditional masterclass format to give students individual attention while building a reputation as an inspiring teacher.
Beginning in 1894, he replaced much of the 19th-century music his student Louis Fleury called "idle twittering" with works by Johann Sebastian Bach and other composers of the 18th century.
Alfredo Casella, who had studied Bach in Italy before coming to Paris, noted that none of his classmates at the Conservatoire knew that composer's music.
This placed him ahead of his contemporaries in awareness of baroque repertoire (his tours had included playing Mozart concertos at the Gewandhaus in Leipzig, a singular honour for a French performer).
Louis Fleury wrote: Bach's sonatas, those wonders, long buried in the dust of libraries, awakened to find a real interpreter [in Taffanel].
Taffanel's duties at the Opéra included directing all new productions, among which during his tenure were French premieres of various Wagner operas and Verdi's Otello.
Founding the Société de musique de chambre pour instruments à vent (Society of Chamber Music for Wind Instruments) in 1879, he revived the wind ensemble music of Mozart and Beethoven while also encouraging the composition of many new works, including Charles Gounod's Petite symphonie.
In addition, during the 1880s, Taffanel participated in "historic" concerts, playing his Boehm flute alongside viola da gamba and harpsichord in performances of baroque music.
These include: He also began writing a method book for flute, 17 Grands exercices journaliers de mécanisme, which was finished after his death by two of his students, Louis Fleury and Philippe Gaubert.
He hated affectation, believing that the text of the music should be respected absolutely, and beneath the supple fluency of his playing there was a rigorous adherence to accuracy of pulse and rhythm.