The construction of the Church of Saint Francis in Cortona was due to brother Elia, the saint's successor to the lead of the Franciscan order who also build Assisi's homonym basilica. The church was built in 1247 in Bagno della Regina a territory that the town had given to Elia's order. Previously, the remains of the ancient Roman spas were in this place.

Unfortunately, the building that had originally been planned and carried out in the Gothic style does not keep much of its ancient structure, which the restructuring performed in the XVII century had widely changed. Only its stretching upwards and its solemnity that are the typical elements of the medieval Gothic style have remained of the original structure. Recently, also the portal and the big windows of the left side of the church have been discovered. A fragment of a XIV-century fresco attributed to the Buffalmacco are still visible on the right wall.
Inside, brother Elia's legacy is still kept. He left some sacred relics belonged to Saint Francis inside the church: his tunic, his hand-written manuscript and his pillow. There is also a fragment of the Holy Cross. According to tradition, it was brother Elia himself, one of Saint Francis of Assisi's most devoted followers in Constantinople, who saved it.
As said above, the inside of the church was affected by restructuring carried out in the XVII century. Particularly, they erased the frescoes that decorated the church in its first years of its existence with a plasterwork. Later, Gothic windows were shut and the altar was substituted. the ancient block of stone that in medieval style was substituted a less austere marble Baroque altar, realized by Bernardino Radi, which keeps the relic of the Holy Cross.
The secondary altars are decorated with late-XVI century works of art: the "Immacolata Concezione" realized by Commodi in 1609 is set on the third altar of the right wall, while the "Miracolo della Mula" carried out by Cigoli in 1597 stands on the fourth altar. The third altar of the left wall, instead, shows a work by Pietro da Cortona, the "Annunciazione", which is considered one of the greatest masterpieces of the Tuscan XVII century. Friar Elia's tomb is in the choir.