Duruflé was affiliated with the Paris Conservatoire, in one capacity or another, for fifty years, beginning in 1920 when he entered the organ class, and ending in 1970 when he resigned as professor of harmony. Even during the hiatus of approximately ten years between his last student exam and the first class he taught in harmony, he served on Conservatoire juries, performed with the Conservatoire orchestra, and was a substitute organ teacher.

Duruflé's earliest experience as a teacher at the Paris Conservatoire was in his unofficial capacity as substitute for Marcel Dupré in the organ class. In 1942 he filled in for Dupré and taught a number of soon-to-be-prominent organists, including Suzanne Chaisemartin, Marie-Claire Alain, Pierre Cochereau, and Marie-Madeleine Chevalier.

In his memoirs Duruflé wrote about his relationship with Dupré. The elder Man

bore an almost familial affection for me, for both of us were Normans… . He followed the course of my studies ever since my time at the maîtrise… .

I did not lose an occasion, of course, to attend all the concerts of this prestigious organist. I would encounter him often in the hallways of the Conservatoire, where he always favored me with a nice smile. One day, in 1942, I believe, he made me an unexpected proposal. “My dear Duruflé,” he said to me, “I must soon leave again for the United States for a tour of six months. Would you agree to substitute for me in my organ class during my absence?” I was at once astonished and very flattered. Indeed, I was not his student. I did not feel myself worthy to accept this honor. At his insistance, I had to accept.

Dupré's students particularly enjoyed playing the Franck works for Duruflé because he had studied them with Tournemire, a student of Franck. They studied his own compositions with him as well, and valued the times when he was substituting. Marie-Claire Alain wrote that by accepting their questions and comments Duruflé was less intimidating than Dupré.