There is no permanent seating in the nave. The little church sits under the large dome. There are two side aisles with chapels.

The basilica was constructed in the Mannerist style and encloses the tiny Porziuncola in its nave. The chiesetta (little church) of Porziuncola (Italian for "Little portion") is the most sacred place for Franciscans. Francis was given this little church, dating from the 9th century, by the Benedictine monks. The church is exquisitely decorated by artists from different periods. Above the entrance is the fresco by Johann Friedrich Overbeck (1829) depicting St. Francis receiving from the Christ and the Virgin the indulgence, known as the "Pardon of Assisi". As vast numbers pilgrims came flocking to Assisi to receive the "Pardon of Assisi", the small space of the Porziuncola became completely inadequate. The necessity grew to build a church incorporating the Porziuncola. The church also incorporated the Chapel of the Transito, the cell in which St. Francis had died.