Although the Conservatoire records indicate that Duruflé was formally admitted to the school on September 12, 1919, it was not until October of 1920 that he played his entrance exam for Eugène Gigout's organ class, performing for a jury comprising Gigout, Charles Tournemire, and André Marchal. Tournemire is quoted as having said of Duruflé: “He will surely be a premier prix, in the style of Marchal.” At age eighteen, Duruflé became the youngest in Gigout's class of ten students, the oldest being thirty-six.

According to contemporary reports, Gigout “played [the organ] in a very clean style, which did not prevent him from performing the music of Franck with great intensity. As an improviser he is reported to have been eclectic, but was drawn particularly to classicism.” According to Fanny Edgar Thomas, writing for The Musical Courier in 1894, Gigout was “one of the most fertile and original masters of that art in the city, indeed being so proclaimed by [Camille] Saint-Saëns, that exacting critic.” Gigout concertized widely in France, Switzerland, Catalonia, and England, and in the course of sixty years he inaugurated some fifty instruments. At the home of Bérenger de Miramon he performed with harpsichordist Wanda Landowska.

When he was thirteen years old, Gigout studied composition at the École Niedermeyer, in Paris, with Saint-Saëns, and was an organ student of Clément Loret, a former pupil of Lemmens. In 1863, he was appointed organist at Saint Augustin in Paris, a position he held until his death. In 1885, he established the École d’Orgue, d’Improvisation et de Plain-chant, and became professor of organ at the Conservatoire in 1911. Gigout gave the first performance of Franck's Choral in A Minor. He published a revised edition, with his own Avertissement, of the École d’orgue by Jacques-Nicolas Lemmens. With good reason it can be assumed that Gigout taught Duruflé according to the Lemmens method, as had Haelling and Vierne before him. Indeed, Gigout was said to have taught his students to play Bach according to the “true Bach tradition,” as the French understood it.