The abbey's origins date back to a funerary basilica (memoria) built to house the tomb of Bishop Albinus (529–550).

The nova basilica was soon named after Saint Aubin, as Gregory of Tours mentions ("Dix Livres d'histoire", l. VI, 16).

In 616, Bishop Bertrand du Mans implied monastic activity: "venerabile Bobeno abbate de basilica sancti Albini", as did the author of the first Vita S. Magnobodi (9th or 10th century): "abbas vocabulo Niulphus qui coenobium".

Excavations carried out in 1997 during the redevelopment of the Musée des Beaux-Arts (Logis Barrault) showed that around this period, the courtyard area of the building was empty of human habitation, and that a few burials were present; the occupation of this period is interpreted as already being the enclosure of the Abbey of Saint-Aubin.

The abbey church was demolished in 1811 to create what is now Place Michel-Debré, and the cloister was incorporated into the new Maine-et-Loire prefecture building.

The fortified bell tower, separate from the abbey and formerly the abbot's own property, has been preserved (the "Tour Saint-Aubin", still visible on rue des Lices).

Beneath the representation of the Maestà, surrounded by two angels, is a painting showing, on the right, the Magi showing the star and setting off towards Jerusalem, on the left, Herod ordering the Massacre of the Innocents, and in the center, Jerusalem symbolized by the representation of the Virgin.

The monks wanted to cover the cloister with a Gothic vault in the 14th century, but this work damaged the Romanesque sculptures.