The construction was started in 1140 to the designs by Giovanni da Gubbio, as attested by the wall inscription visible inside the apse.
It was on hearing Francis preaching in this church in 1209 that Clare became deeply touched by his message and realized her calling.
Tommaso da Celano related[1] that once Saint Francis was witnessed praying in this church while, at the same time, he was seen jumping on a chariot of fire in the Porziuncola.
The rather bare top level is triangular with an empty semi-circular arch in the middle, probably intended to contain a frieze or a mosaic.
The bottom and the middle part of the square bell tower, on the left side of the façade, were built in the 11th century.
On the right aisle is the Chapel of the Blessed Sacrament in Baroque style (begun in 1541 and enlarged in 1663), partly frescoed in 1663 by the local painter Giacomo Giorgetti, a pupil of Giovanni Lanfranco.
In the apse stands the majestic choir, with 22 stalls, decorated with wooden carvings by Giovanni di Pier Jacopo da San Severino (1520).
There are several paintings by Dono Doni: Christ adored by Saints (1555); on the two altars on both sides of the major one, there are two more works: Deposition (1562) and Crucifixion (1563).
Under the cathedral there is a crypt with the pagan Roman sarcophagus from the 3rd century, asserted to have once contained the remains of Saint Rufinus.
It bears across its front, as many sarcophagi do, a bas-relief with the myth of Diana and Endymion, offering a pagan vision of tranquil afterlife.