The basilica was situated at the confluence of the Rhône and the Saône up to the end of the 18th century when the engineer Perrache pushed the junction of the two rivers to the south by encompassing the Island of Mognat.

From the beginning of the Christian era, various chapels and monastries succeeded each other on the site before present abbey was built and consecrated in 1107 by Pope Pascal II. In addition to the superb 12th century Romanesque capitals, we notice, at the transept crossing, four monolithic columns dating from Roman times and originating in the ancient altar of Rome and Augustus in the Croix-Rousse.