The Lower Basilica is one of the two temples that make up the main St. Fransciszek. There is a crypt in which there are the remains of the saint and his closest brothers. The crypt is richly decorated with frescoes by the most outstanding Italian artists from the fourteenth century. They depict scenes from the life of Jesus and St. Francis.
A 13th-century portal topped with a rosette leads to the crypt. It is preceded by a porch created by the sculptor Francesco di Bartolomeo da Pietrasanta. It consists of an arch supported by two columns with an attic decorated with mosaics depicting scenes from the life of St. Francis.
There are 5 chapels adjacent to the nave, also decorated with frescoes. In addition, on the right side of the nave there is a passage to the so-called Of the Chapter Room, known as the Chapel of the Relics. It was built in the first half of the 13th century. It houses the relics of St. Francis.