Quef was born in Lille, France, and studied at the conservatory there before entering the Paris Conservatoire where he studied with Guilmant, Vierne, and Widor. He served several smaller churches until 1898 when he was appointed as assistant organist at La Trinité in Paris. Four years later, he became the organiste titulaire at the same church, following the resignation of Guilmant. He remained at that post until his death in 1931.