The first monks belonging to the Order of San Francisco arrived in Baena in 1550 under the patronage of María Mendoza y Sarmiento, wife of the first duke of Baena, and built the San Francisco church, cloister and monastery, although the structure we see today dates from the 17th century. The church has a single nave culminating in a crossing and is covered by a barrel vaulted ceiling with lunettes and transverse arches. Paintings with rocaille decoration adorn all the walls, creating an impressive appearance.
The main church portal is very simple and dates from the 18th century. Two Tuscan pilasters flank the flat-arched door. The portal on the side street is even simpler, with a full pediment and pyramid-shaped pinnacles from the 17th century.
The main altarpiece dates from 1740 and is made of polychromed carved wood. The church has a magnificent statue of Jesus of Nazareth, the head of which was carved in the Baroque style between 1701 and 1733 by Miguel de Perea of the Sevillian School.