The large semi-circular apse of the Basilica contains an impressive choir of wood, designed by the friars of Santa Maria in the 1600s.

The pulpit also made of wood, displays fine Baroque carvings which recount episodes of the story of the Indulgence of Assisi.

The High Altar, of Siamese yellow stone, is adorned by seven bronzes representing Christ among several Franciscan saints.

The two ambos (reading stands), situated to the sides of the presbytery are decorated with scenes from the life of St. Francis.

Under the High Altar is the Crypt, in which there are some remains of buildings which may have formed part of the old living quarters of the friars of the Porziuncola, and which came to light during archaeological excavations undertaken in 1966.