Berthier was born in Auxerre, Burgundy; both of his parents were musicians - his father Paul was the kapellmeister and organist at the Auxerre Cathedral. Learning first from his parents, Berthier was trained in music at the César Franck School in Paris. While there, he was taught by, among others, Edward Souberbielle and Guy de Lioncourt (whose daughter he married). In 1955 Berthier was first asked to compose music for the Taizé Community, which was then just a monastic community of twenty brothers. Six years later he became organist at the Church of the Jesuits in Paris, Saint-Ignace, where he worked until his death. In 1975, Berthier was again asked to compose for Taizé, this time for chants to be sung by the increasing numbers of young people coming to worship there. Over nearly twenty years, Berthier built up a body of church music that has been utilized around the world. He died at his home in Paris in 1994, and requested that none of his own music be used in his funeral at Saint-Sulpice. His son is Vincent Berthier de Lioncourt.