[3] The Abbot Pierre's account tells that during a hunting expedition in 976, Countess Emma, the wife of William IV, Duke of Aquitaine, discovered the ruins of a chapel dedicated to Saint Hilaire and decided to found an abbey at the site.

Father Gausbert, cousin of Countess Emma, brought thirteen monks from Église Saint-Julien de Tours to create a Benedictine abbey, first settling in Saint-Pierre-le-Vieux, Vendée, about 2 kilometres (1.2 mi) north of the current ruins.

In May 1197, by the bull Officii nostri, Pope Clement III took the monastery of Maillezais under papal protection, listing all of its dependencies and properties.

Excommunicated from the church, he went to Rome and apologized to the Pope in the presence of the abbot of Maillezais for his wrongful deeds.

The area was extensively developed in the early part of the 13th century, when the abbeys of Maillezais, Nieul-sur-l'Autise, Saint-Michel-en-Herm, and the Absie St. Maixent joined together for the project.

In 1317, after the final suppression of the Albigensians in France, Pope John XXII restructured the allocation of French bishoprics, creating two new episcopal sees, each with a cathedral, out of the diocese of Poitiers.

The cathedral became a center of intellectual pursuits; in the early 16th century François Rabelais taught at the abbey for five years.

There were many improvements to the cathedral's interiors such as better furnishings, conversion of the abbot's residence into an episcopal palace, building of a monastery dormitory near the second cloister.

In 1589, Agrippa d'Aubigné, a Protestant, a scholar and a poet, became the bishop[citation needed] and fortified the cathedral with a watch tower.

When during the late 16th and early 17th century the Protestants of the Huguenots had converted it into a fort-like structure, the Catholics had to even baptize their children outside the city limits.

[4][6] The cathedral site remained dormant till after the French Revolution when it was sold as national property to serve as a stone quarry.

[4] The façade on the west gable of the church built in 1025, which consisted of two bays of naves flanked by two towers, is now fully open.

A pier provided the approach to the moors which could be used for plying boats through its winding channels from where one can get views of the "imposing ruins of the abbey silhouetted in the sky".