Michel Chapuis' career as organist and as specialist in performance upon historically important instruments began at Cathedral of Dôle when he was quite young.
He proceeded to study music in Paris; his teachers included Eduoard Souberbielle for organ, René Malherbe for composition, and Emile Poillot. In 1951, while studying under Marcel Dupré at the Conservatoire de Paris, Chapuis took first prize in organ and improvisation (the Prix Périlhou et Guilmant). He served as organist for the Paris churches of St. Germain l'Auxerrois (1951-1954) and St. Nicolas des Champs (1954-1972), accompanied at Notre Dame from 1955 to 1964, and was titular organist of St. Séverin from 1964. At the same time, he has held organ teaching posts at the prestigious conservatories of Strasbourg (1956-1979), Besançon (1979-1986), and finally Paris (1986-1995). In 1995, Chapuis was named organist to the Versailles Royal Chapel. Both Chapuis' life as a teacher and as a performer have been dedicated to historically informed performance; his greatest contribution has been in musical interpretations upon historic instruments. In addition to performances of every surviving piece of French organ music from the seventeenth and eighteenth centuries on the Cliquot organ of St. Nicolas des Champs, he has produced numerous recordings matching early repertory to historic instruments: Daquin Noëls on the 1710 Silbermann organ of Marmoutier, Couperin on the 1772 organ by Brother Isnard of Tarascon in Saint-Maximin, Marchand on the 1782 Cliquot organ at Souvigny. Chapuis has also personally supervised several instrument restorations across France.