With the general reorganization of the structure of the French church by Pope John Paul II, Saint-Flour became the suffragan of the Archdiocese of Clermont.

Like many French bishops, he was compelled to face the problem created by the dwindling number of priests in the Roman Catholic Church.

In two documents concerning the foundation of the second monastery of St-Flour, drawn up in 1013 and 1031, and in a letter written to Pope Urban IV in 1261 by Pierre de Saint-Haon, prior of Saint-Flour, St. Flour is already considered as belonging to the Apostolic times, and the Speculum sanctorale of Bernard Gui in 1329 relates at length the legend of this "disciple of Christ".

[3] Amblard de Brezons, his nephew, surnamed "le Mal Hiverné", seized the monastery and destroyed all of it except the church.

Among his successors were Pierre d'Estaing (1361–67), afterwards Archbishop of Bourges and cardinal in 1370; and Louis-Siffrein-Joseph de Salamon (1820–29), former counseiller-clerc to the Parlement of Paris, who during the French Revolution had secretly acted in France as the pope's agent, a rôle concerning which he has left very important memoirs.

[6] During the French Revolution, the National Constituent Assembly reformed the Church in France, drawing up the Civil Constitution of the Clergy (12 July 1790).

[7] All clergy were obliged to swear an oath of allegiance to the Constitution,[8] thereby effectively entering into a schism with the Papacy and the Roman Catholic Church.

The legitimate bishop of Saint-Flour, Ruffo de Bonneval, refused to take the oath to the Constitution, and therefore his seat was declared vacant.

[9] The diocese was re-established by the Holy See in accordance with canon law and the Concordat of 1801, which had been agreed by First Consul Napoleon Bonaparte and Pope Pius VII.