The Franciscans had occupied a modest house in the city called Santa Maria delle Pugliole, founded in 1211 by Bernard of Quintavalle, one of the first members of the Order.

At the urging of Pope Gregory IX, the authorities of the medieval commune gave the property on which the basilica is now built to the friars in 1236 for a church of their own.

[2] During the occupation of Italy by the French Revolutionary Army, in 1796 the church was desecrated and the friary was seized and used as a barracks by the occupying forces.

The 14th-century chronicler of the friary, Bartolomeo of Pugliole, recorded that, when the vault of the apse collapsed in 1254, the restoration work was supervised by one Friar Andrea Maestro della Ghiexia, who is described as "of the twisted legs".

This is manifest in the interior, which has a nave and two aisles, in the apse with corridor, in the high vaults divided into six sections (like in Notre-Dame de Paris) with ogival arches, and in the use of buttresses.