At the end of the 16th century, Magdalena de Ulloa, Juan de Austria's tutor and Luis de Quijada's wife (Charles V's butler, Luis de Quijada), founded the school of the Society of Jesus next to the disappeared house of the Riva Herrera as she did in other cities. This last-mentioned house was the only one that accepted the monarchs when they arrived in Santander. Nowadays, the church is the only building left. It is stated that the building was founded in 1595, the year in which the project was presented. However, its construction started in 1607. It was finished around 1620 because Santander's school was against it. This work is attributed to Juan de Nates and Alonso de Tolosa, both architects of the Order. The temple's construction began in 1607 but the process was stopped between 1617 and 1619. In 1637, the church's patronage, dedicated to the Annunciation, was given to the Marquis of Villapuente, José de la Puente y Villa Castejón. This school meant a new urban space in Santander. The Plaza Nueva was opened and some buildings, that represented better the socioeconomic forces of the time were established around it. The Jesuits not only attended the temple's works and the formation offered in the school but also trained different departments such as the predication, the sick's assistance, the missions and confessions. Its activity finished with the Decree of expulsion applied by Charles III.

La Compañía abandona el edificio, tras el Decreto de expulsión y no volvería a Santander hasta 1850, durante el reinado de Isabel II (1833-1868), esta vez ocupando unas casas particulares. Con el aumento de sus actividades se plantean adquirir casa propia, a finales del S.XIX se establecen en la que es actualmente, la Iglesia y residencia del Sagrado Corazón.