The castle began life as a fortified rural church built of masonry and lime mortar, with an irregular basilica-type layout featuring a displaced quadrangular chevet on the left-hand side (a defining characteristic of churches with a “twisted” chevet). It had three naves, the central of which was the widest, demarcated by arcades supported by pillars and columns whose capitals were decorated in the late Romanesque style. The church did not have a crossing. 
On the north side of the church’s exterior, archaeological excavations revealed part of a U-shaped moat dug into the ground to an approximate depth of 2 metres, and a drystone wall standing directly above the moat that may have served as an outer wall creating a narrow bailey.

The excavations also revealed the existence of numerous burials both inside and outside the church, the majority of which were in and around the chevet. The bodies had been buried in trapezoidal or anthropomorphic tombs (some featuring markings in the head area) that had been dug into the rock and covered with mounds of earth or in some cases, stone slabs. Of particular note is one grave that was partially covered by a large ceramic vessel.

Around 1368, this early building was burned down by the Nasrid forces of Muhammad V, an ally of King Peter I, as part of the conflict between the Castilian king and his half-brother Henry II of Trastámara.

Subsequently, a new church was built on the same layout as the previous one, albeit with some modifications. Two towers were constructed: the Torre de San Miguel, or St Michael’s Tower, at the far end of the church; and the Torre de Santa María, or St Mary’s Tower, incorporating the chevet (which now had a semi-circular interior).

This new fortified structure was encircled by the walled enclosure we can see today, which has an irregular pentagonal layout and boasts five corner towers built of solid masonry. It was further defended by an outer wall, barbican and moat. Inside the bailey, the new fortified church was rebuilt along the lines of an alcázar, or fortress, with two large towers linked by two curtain walls with a broad parapet and loopholes, held up by semi-circular arches resting on buttresses.
In terms of function, the church was divided into two distinct sections: the lower section was for religious use, and the upper section served a military purpose. The section for religious use was divided into three naves, of which the central was the widest. The church was surrounded by a large terrace that served as a bailey and provided access to the defensive features on the walls and the Torre de Santa María. At that time, burials were concentrated outside the church, specifically in the area around the chevet, with the exception of two sepulchres located inside the church next to the large arch leading onto the apse area (the most sacred part of the new church building).

Between the end of the 15th century and the first half of the 16th century this fortified church was converted into a palatial castle. The work involved building two large structures and a small porticoed courtyard with three basket-handle arches with Renaissance-style capitals. This courtyard served as the hub of the noble residence and a number of rooms led off from it. 

The apse area of the church was converted into a chapel by Juan Pacheco, the Commander of Lopera, in 1535. It was covered by a cloister-vaulted ceiling and decorated with Renaissance-style plasterwork and painted inscriptions, and could also be accessed via the outer courtyard through a new entrance that was created in the north façade and sheltered by a portico supported by columns.

The archaeological excavations revealed that there was a garden area outside the building, with a large courtyard incorporating a fountain fed by a waterwheel. There was also a vegetable garden, thus confirming that the building had been used as a residence. 

In the 20th century the castle was used as both a dwelling and a wine cellar; numerous wine presses dating from this period are conserved, buried to the west of the Torre de San Miguel (disrupting the archaeological layers of the site in the process).

A number of Bronze and Iron Age sites have been found in the area around Lopera, along with settlements from the time of the Low Roman Empire that remained inhabited through to the Visigothic era. Other discoveries date back to the time of the emirate, when a communal refuge on Cerro de San Cristóbal was established by the inhabitants of local settlements including the hamlet of Lopera (which may correspond to the place referred to as Bayyara in Muslim sources). The archaeological excavations carried out in Lopera’s historic town centre have confirmed the existence of this hamlet, which was home to communities that farmed this area during the 12th and 13th centuries. 

After the Christian conquest, around 1240-1241, Lopera was given to the Order of Calatrava, which created the Commandery of Lopera and subsequently strengthened the castle’s original defences between the 14th and 15th centuries. The Order amassed an extensive feudal estate in the south-west of what is now the province of Jaén, encompassing large swathes of the Campiña region and the foothills of the Sierra Sur mountains.

Moreover, as the estate bordered the kingdom of Granada, the Order had to extensively fortify its landholdings. 

This network of fortifications played an important role in securing the border during the process of territorial expansion carried out by the Castilian armies in the 13th and 14th centuries, and came to prominence once again during the second half of the 15th century within the context of the conflicts between noble families that broke out during the reign of Henry IV of Castile. The members of the Order played an active role in these clashes between the followers of the king and the supporters of a coalition of noblemen led by Pedro Pacheco, the Marquess of Villena, and Pedro Girón, the Master of the Order of Calatrava. During the conflict, Lopera Castle was attacked and sacked in 1466 by the allies of the Constable of Castile, led by Pedro de Escavias, Mayor of Andújar. Subsequently, it was declared an independent villa by Philip II in 1595.

As a result of the expropriations that took place during the 19th century, most of the church’s possessions were acquired by members of the merchant class. The castle passed into the hands of Alonso de Valenzuela, a Member of Parliament and Mayor of Lopera, in 1856.

During the Spanish Civil War, Lopera once again became embroiled in conflict, as the dividing line between the Nationalist and Republican forces (popularly known as the Andújar Front) was located on the outskirts of the town. Numerous traces of this conflict can still be seen in and around Lopera, including machine-gun nests, Republican trenches, an anti-tank bunker, and cellars and caves used as air-raid shelters. The most significant episode was the Battle of Lopera, which took place from 27 to 29 December 1936 and resulted in the seizure of the town by rebel troops.

Lastly, in the 20th century the castle was used as a wine cellar and served as a temporary residence; in order to enable these new uses, substantial alterations to the original fortified structure were made and the castle complex underwent irreversible changes.