It was formed in the last Ice Age (see Pleistocene), when the Rhône Glacier reached as far as the Jura mountains.

In the late nineteenth century, following the engineering works of the Jura water correction, the water-level of the three lakes of the Seeland have dropped enough to clear the until-then hidden isthmus, linking Cerlier to St. Peter's Island, which has ever since become a peninsula, although separated from the shore by a canal.

Before his expulsion, Jean-Jacques Rousseau spent two months on the island in 1765, calling it the "happiest time of his life".

Traces of Merovingian graves, a Carolingian wooden monastery and an abandoned 11th century basilica[3] have been discovered near the current building.

Over the following years the priory building was used as a sheep farm and an inn and it was extensively modified, renovated and rebuilt.