The basilica was constructed in the Mannerist style between 1569 and 1679, enclosing the 9th-century little church, the Porziuncola, the most sacred place for the Franciscans.

It was here that the young Francis of Assisi understood his vocation and renounced the world in order to live in poverty among the poor, and thus started the Franciscan movement.

The buildings around the shrine were taken down by order of Pope Pius V (1566–1572), except the Chapel of the Transito, the cell in which St. Francis had died.

[2] The work progressed slowly, due to a constant lack of money, as the building was financed with donations.

On 15 March 1832 the central nave, a part of a lateral aisle, and the choir collapsed during a violent earthquake.

On 11 April 1909, the church was raised by Pope Pius X to the status of "patriarchal basilica and papal chapel".

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”.

The most outstanding work is the six-part fresco in the apse of this little church, painted by Ilario da Viterbo (1393).

On the walls there is a fresco by Giovanni Spagna (1520), depicting the earliest followers of St. Francis, with their names above each portrait (Ruffino, Leone, Masseo and Egidio).

The crypt's altar rests on a massive, multiple-branched tree trunk, sculpted by Francesco Prosperi.

Behind the altar stands an enameled, terracotta, bas-relief tabernacle by Andrea della Robbia, expressing with an extreme finesse the emotions of the figures.

It was decorated between 1506 and 1516 with a series of frescoes by several painters, including Umbrian Tiberio d'Assisi who depicts the early Franciscan community and the first saints of the order, the miracle of the roses, and the concession of the indulgence The little friary houses the museum of the Porziuncola with many religious objects, archaeological finds, and a noteworthy collection of paintings: