In 1948 he was appointed organist at the Protestant Church of Montreux, where he lived together with his wife, Gertrude Junod-Burger.
Though he has edited many volumes of other early music (e.g. Andrea Gabrieli and Girolamo Frescobaldi), he is generally known as a specialist in the history of the Huguenot psalter.
His magnum opus is the two-volume edition of text and melodies of this Psalter: Le psautier huguenot du XVIe siècle, i: Les mélodies; ii: Documents et bibliographie (Basle, 1962).
He contributed music, harmonisations and texts to the new hymnal of the French-speaking Reformed Church of Switzerland (1976).
In this hymnal also many texts of his brother, Edmond Pidoux, literature professor in Lausanne, are present.