Hugues de Salins, who redesigned St. John's, also led the reconstruction plans for St. Stephen's between 1033 and 1050.

Between 1253 and 1254, Archbishop Guillaume de la Tour unified the two chapters, a decision which was ratified by Pope Innocent IV on 1 August 1254.

[2] After the Battle of Besançon in 1575, masses were held at both cathedrals to celebrate the Catholic victory against the Protestants.

[3] From 1668 to 1675, St. Stephen's Cathedral was abandoned and it was later decided that it should be destroyed, along with some surrounding houses, to allow for the construction of the Citadel of Besançon,[4] after Franche-Comté was given to Louis XIV of France in the Treaties of Nijmegen.

[5] However, it was then decided that the cathedral should remain, but it was stripped of its contents, and then destroyed in any case after an accidental fire, when construction of the citadel began.