Interior of the Basilica
The basilica is composed of a nave and two side aisles, as well a series of side chapels. 

It is simple yet elegant, with only a few friezes and decorations, since it was built during the time of the Reformation. In later years, stucco work was added to embellish
the side chapels and the noble families of Assisi contributed to pay for this. 
The building was damaged extensively by several earthquakes and, as we mentioned before, the earthquake of 1832 greatly harmed the structure. Towards the end of
the Sixties, the flooring was redone inside the basilica and the crypt under the choir and altar area was built. 

The Chapel of the Passing  

Like the Chapel of the Porziuncola, the Chapel of the Passing is also highly significant. 
This is where St. Francis died on the evening of October 3, 1226, surrounded by the brothers who were dearest to him. During the time of the first Franciscan settlement
there, it was used as an infirmary, despite its small size. 
It seems that the little side door is the original one dating back to the time of St. Francis. Inside the chapel are frescoes by Giovanni Spagna, depicting the companions of
the Poor One. The friars’ names are listed above each portrait. 
There is a statue of the saint on the altar and this terra-cotta work, done by Andrea Della Robbia, dates to the end of the fifteenth century. 
 
Apse
 
The original plans, which indicated a square apse, were modified and a semicircular one was built in its place. The presbytery was rebuilt recently and elevated in order

to open up the crypt beneath the altar.
What is most striking about the apse is the wooden choir, which was started in 1689 and was constructed entirely by the friars under the careful guidance of Brother
Louis of Selci. It is made of walnut. The central part of the apse is dominated by the pontifical altar, which is the work of the architect Apolonj-Ghetti and features
low-reliefs by E. Manfrini.

The Crypt 

This was constructed recently in order to highlight the remains of the most ancient Franciscan constructions that were present there. The windows are the work of
Alberto Farina and the altar was sculpted by Francesco Prosperi, an artist from Assisi. 
 

The Della Robbia Tabernacle  

This is an enameled terra-cotta polyptych done by Andrea Della Robbia. Depicted in the center of the upper section is the Crowning of the Madonna. On the left is St.
Francis receiving the Stigmata while St. Jerome is portrayed on the right-hand side. Portrayed in the lower section, going from left to right, are: the Annunciation, the
Birth of Jesus in the grotto in Bethlehem and the Visit of the Magi. 

The Sacristy

The woodwork done by the Franciscans in the sacristy is outstanding. This is the work of Brother James of Borgo San Sepolcro and it was completed with great artistry

during the second half of the seventeenth century. The ceiling, which was restored during the Forties, also reveals outstanding workmanship.