The Society of Jesus arrived in the city of Badajoz in 1633. They settled in a convent that already existed: the convent of Santa Catalina. This convent, which was founded in 1515, was abandoned by the nuns in 1623 because it was severely damaged. Some sources state that the Jesuits restored the building in 1634 and settled in it at the initiative of Alonso Pérez de Vita, a graduate and canon penitentiary. They bought the adjoining houses and created a small square in front of the old church's façade, which had been dedicated to Santa Catalina and, then, to San Antón. This square is currently known as the Santa Maria Square. They also bought the building at the other side of the current Soto Mancera Street. They placed a joining arch to make easier the way between the residence and the college. This building was later called "Casa de las Aguas". The College received several donations from different distinguished figures from the city that helped in its development and maintenance. The same happened with the church, so some of these figures had the permit to use it as a funeral pantheon. Some of these personalities were Damiana de León y Silva, who contributed in the construction of the temple's reredos, or Juan Solano de Figueroa, a canon and author of the ecclesiastical history of Badajoz, who donated his complete library to the college in 1661. In 1767, the Jesuits had to abandon the building due to Charles III's Decree of expulsion (1759-1788). By then, the college counted on a Grammar teacher and two Ludimagistri.

After the expulsion, the complex that gathered a college, a convent and a church was given to some individuals. The convent and the residence were turned into homes. The parish of Santa Maria la Real was settled in the temple until Mendizábal’s secularization, when it was delivered to some individuals. In 1997, the school was demolished to build the students residence Julio Cienfuegos. The convent was restored in 2001 and it turned into the headquarters of the Department of Culture in 2010.