Following an earthquake, reconstruction of the basilica started in 1836 by the architect Luigi Poletti and it was finished in 1840. He remodeled the façade in a Neoclassical style. Between 1924 and 1930 this façade was rebuilt by Cesare Bazzani in a Baroque style, more ornate than the original.

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.