On the façade of the church are the crests of the Basilica of Saint Francis (which the sanctuary depended upon) and, above the main door, the phrase: "Hic primordia Fratrum Minorum" (Here the beginnings of the Friars Minor), which recalls the tradition, according to which Saint Francis drew up the foundations of Franciscan Rule.

The inside of the church has three aisles, separated by polygonal columns. Here you will find the humble hovel, "tugurio di somma umilitate", on the site where it was discovered, the place the saint took refuge with Bernardo da Quintavalle and Pietro di Catanio. It is formed of three small rooms, the second of which is used as a chapel, with a fifteenth-century communion altar on an octagonal cippus. In the church, on the counter-façade, is a painting of Saint Michael Archangel by Domenico Mattei. On the walls are paintings by Cesare Sermei alluding to Franciscan history.