It was built around 1565 to replace the original Basilica of Saint Justus, the site of the coronation of Pope Clement V in 1305,[2] which had been destroyed in 1562 by the Huguenot captain François de Beaumont.
After the destruction of the original Basilica of Saint Justus in 1562 by the Huguenot captain François de Beaumont, the canons decided to rebuild their collegiate church within the walls of the city.
Construction began in 1565 and continued till 1663—at first rapidly, as the canons of the basilica wanted to celebrate a Mass by Christmas 1565—then slowed down for lack of money.
The choir has a painting of the Annunciation by Hyacinthe Collin de Vermont and a Nativity by Hughes Taraval.
The stained glass windows depicting the life of Saint-Just and early Christianity in Lyons which dates from the 19th century.