Saint Francis is one of the most venerated of all Christian saints. Born in 1182, he chose a religious life after a youth filled with empty pleasures and frolicking. He was followed by a considerable number of disciples, who congregated in Portiuncula, a small hermitage in the foothills of Assisi where Francis spent most of his life, and where he died in 1226. Portiuncula is also the site of the miracle traditionally associated with this painting, which is based on a legend from the life of Saint Benedict. Its origins date back to the fourteenth century, although it was only exploited during and after the Catholic Counter-Reformation, when the traditional iconography that depicts Francis as a saint in harmony with the world was transformed to present him as an ascetic, emphasising his visionary episodes and his inclination towards the sacrifices of penance. In that episode, burdened with the cardinal sin of lechery, Francis decided to roll over some thorn bushes to assuage his carnal appetites with pain. Legend has it that red roses sprang up where drops of his blood hit the ground, and that he used their blossoms as a votive offering at Portiuncula. Francis later petitioned Pope Innocence III for full plenary or Jubilee indulgence for all those who made a pilgrimage to the hermitage.

Saint Francis of Assisi in the Portiuncula c.1601–03, depicts Francis in a state of rapture as the Virgin, Saint John the Baptist and a band of angels appear to him. The customary interpretation is that the saint was praying for divine intervention to obtain indulgences for all who visited the hermitage, although this image contains none of the traditional iconographic elements associated with the so-called Jubilee of Portiuncula, such as roses or a depiction of Francis lying on thorn bushes.

Moreover, Ludovico Carracci eschews the ongoing tradition of portraying that scene inside the hermitage, opting instead for an outdoor setting at night.

This painting has also been linked to a drawing by the same artist, now at the Musée du Louvre, Paris, in which the saint`s gestures are more exaggerated -arms open, rather than crossed over his chest- and Christ points to heaven, rather than to the saint. Given that the painting invites the viewer to adopt Francis`s pious and concentrated attitude towards his vision, it seems likely that Ludovico was actually depicting one of Francis`s many visions, which were more the basis for his canonisation in 1228 than the Jubilee of Portiuncula.

The influence that Raphael, Correggio and Venetian painting had on Ludovico, Agostino and Annibale Carracci is evident in this work from the Museo del Prado, a paradigm example of the classical balance that dominated their compositions, combined with the naturalist tendency they defended at their Accademia dei Desiderosi in Bologna, which became the Accademia degli Incamminati in 1590. By freeing artists to rediscover what the Carracci called il vero naturale (the truth in nature), this institution was of crucial importance to the launch of the classical branch of Baroque painting. Saint Francis of Assisi in the Portiuncula was attributed to Agostino Carracci until Alfonso E. Pérez Sánchez identified it as the work ascribed to Ludovico in the inventory of paintings that Charles IV kept at the Casita del Príncipe in El Escorial, Madrid. The King himself may have acquired it in Italy while he was still Prince of Asturias. It may originally have been commissioned as decoration for a chapel at the Palazzo Zambeccari in Bologna, shortly after Luigi Zambeccari married Pantasilea Bentivoglio (Riello, J.: Italian Masterpieces. From Spain`s Royal Court, Museo del Prado, 2014, p. 96).