The range and quality of the works give the basilica a unique importance in demonstrating the outstanding development of Italian art of this period, especially if compared with the rest of Christian Europe.

On 16 July 1228, Francis was canonized by Pope Gregory IX in Assisi, and he laid the foundation stone of the new church the following day, although construction may already have been begun.

On 27 October 1986 and January 2002, Pope John Paul II gathered in Assisi with more than 120 representatives of different religions and Christian denominations for a World Day of Prayer for Peace.

While a group of specialists and friars were inspecting the damage to the Basilica of Saint Francis, an aftershock shook the building, causing the collapse of the vault.

Much of the cycle of frescoes of the life of Saint Francis by Giotto in the Upper Church of the Basilica were slightly damaged whereas those of the sections of the vault which collapsed were almost entirely destroyed.

Architecturally, the exterior of the basilica appears united with the Friary of St. Francis, since the lofty arcades of the latter support and buttress the church in its apparently precarious position on the hillside.

The Lower Church was built entirely in the Romanesque style, having low semi-circular ribbed cross-vaults over the nave and barrel vaults over the transept arms.

The main entrance to the nave is through an ornate Gothic doorway built between 1280 and 1300, and later enclosed with a simple Renaissance style porch of 1487 by Francesco di Bartolomeo da Pietrasanta (d. 1494).

There is a single large doorway in the Gothic style, divided by a column and with a rose window set in the tympanum above the two cusped arches.

The work proceeded with a number of different projects and appears to have involved numerous artists, some of whom are as renowned as Cimabue and Giotto, but many of whom are no longer known by name.

This bright and spacious basilica consists of a single four-bay nave with cross-vaulted ceiling bordered with patterns of crosses and leaves, a transept and a polygonal apse.

The upper part on both sides of the nave, badly damaged by the earthquake of 1997, was decorated in two rows with in total 32 scenes from the Old Testament (starting with Creation of the World and ending with Joseph forgives his brothers) and the New Testament (from the Annunciation to The Women at the Tomb), while the upper register of the entrance wall is covered with two frescoes Pentecost and Ascension of Jesus.

Since it took about six months to paint one bay of the nave, different Roman and Tuscan masters, followers of Cimabue, have performed this series of scenes such as Giacomo, Jacopo Torriti and Pietro Cavallini.

Pietro Cavallini had painted around 1290 a similar fresco Isaac blessing Jacob in the convent of the church Santa Cecilia in Trastevere in Rome.

The first span of the ceiling is decorated with frescoes of the "Four Doctors of the Church“ ( Jerome, Augustine, Gregory and Ambrose), attributed either to a young Giotto or to one of his followers.

The third span presents four heart-shaped medallions of the Christ, Mary, John the Baptist and Francis, painted by Jacopo Torriti.

On the left wall of the porch stands the bust of Pope Benedict XIV who granted this church the title of Patriarchal Basilica and Cappella Papale.

Above this last burial monument stands a statue of the Blessed Virgin and on its left the figure of a crowned woman seated on a lion, made by Cosmatesco (1290).

The niches in the wall contain the burial monuments of the Governor of Spoleto (by then part of the Papal States) Blasco Fernandez and his son Garcia, both assassinated in 1367 (anonymous local artist, 14th century).

As the popularity of this church increased, side chapels for noble families were added between 1270 and 1350, destroying the frescoes on the opened walls.

It was built by the Franciscan Cardinal Gentile Portino da Montefiore and was decorated between 1317 and 1319 with ten frescoes depicting the saint's life by Simone Martini.

This dedication most likely referred to the Cardinal's position as Cardinal-Priest of the Basilica of St. Martin "ai Monti" in Rome, and was intended to be his burial place.

The chapels on the right are dedicated to Saints: The nave ends in a richly decorated semicircular apse, preceded with a transept with barrel vaulting.

The frescoes in the right transept depict the childhood of Christ, partly by Giotto and his workshop and the Nativity by the anonymous Maestro di San Nicola.

The funerary monument is set in a niche above the altar, with the recumbent effigy of a young man placed inside a mortuary chamber and flanked by two angels.

Between the tomb and the stained glass window appears a frescoed triptych attributed to Giotto's school, representing the Madonna and Child with Saint Francis and Nicholas.

Once featuring frescoes depicting an allegory of the Crucifixion by Stefano Fiorentino (destroyed in 1622), the walls of the apse are now covered with a "Last Judgment" by Cesare Sermei di Orvieto (1609–1668).

His remains had been hidden by Brother Elias to prevent the spread of his relics in medieval Europe, a story told by Jon M. Sweeney in The Enthusiast.

This woman of Roman nobility, affectionately referred to as "Brother Jacoba", was the most faithful friend and benefactress of Saint Francis.

Next to the basilica stands the Sacro Convento friary with its imposing walls with 53 Romanesque arches and powerful buttresses supporting the whole complex.