Jacopone was connected with the latter group and in 1294 they sent a deputation to Celestine V to ask permission to live separate from the other friars and observe the Franciscan Rule in its perfection -- a request which was granted. On Celestine's death in 1297 the position of the Vatican reversed: Boniface VIII favored the Franciscan regulars which opposed The Spirituals strict views. Jacopone, in response, signed a covenant with the powerful Colonnas, one of the most influential families in Rome, calling for Boniface's deposition. The Pope excommunicated them. A battle between the two rival parties ensued, ending with the siege of Palestrina and the imprisonment and excommunication of Jacopone in 1298. He was freed in 1303 on the death of Boniface, having being excluded from the Jubilee of 1300 by papal bull. He retired to Collazzone, a small town situated on a hill between Perugia and Todi, and died in 1306.
Jacopone was steadfast in condemning corruption, especially through his satirical Italian poems. Jacopone would not recant his position on the requirement of ascetic poverty, believing that the mainstream church had become corrupt and that its ministers were not interested in the welfare of the poor. This criticism is echoed in the contemporary Alleluia Movement. It was a time of famine and poverty in Italy, and many mystics and preachers like Gioacchino da Fiore anticipated the end of the old world and the coming of Christ because kings and clergy had become too attached to material goods, too interested in their personal wars rather than the welfare of the country. Jacopone's preaching attracted many enthusiasts even within the Franciscan order and Dante praised him in his Paradiso.
Jacopone's body is buried in a crypt in the church of San Fortunato, Todi.
Some of his laudi were especially in use among the so-called Laudesi and the Flagellants who sang them in the towns, along the roads, in their confraternities, and in sacred dramatical representations. With hindsight, the use of the laudi may be seen as an early seed of Italian drama that came to fruition in later centuries.
The Latin poem Stabat Mater Dolorosa is often attributed to Jacopone, although this has been often disputed. It is a fine example of religious lyric in the Franciscan tradition. It was inserted into the Roman Missal and Breviary in 1727 for the Feast of the Seven Sorrows of the Blessed Virgin Mary, celebrated on the Friday before Good Friday. Following changes by Pius XII, it now appears on the Feast of Our Lady's Sorrows celebrated on 15 September. Many composers have set it to music, including Josquin des Prez, Giovanni Palestrina, Giovanni Battista Pergolesi, Gioacchino Rossini, and Antonín Dvořák.