Since the exclaustration of the Augustinian friars, the convent has suffered a great deterioration, the diocese rescuing the property after the signing of the Concordat of 1851, when Don Ramón Vargas was ecclesiastical governor. The building is recovered as a mission house and spiritual exercises for the diocesan clergy. The Diocese of Guadix, through the Conciliar Seminary of San Torcuato, purchased the Alcazaba from Mr. Felipe Ramírez de Aguilera y Bercín, as stated in the deed of sale dated January 18, 1868, granted before the Notary Public of Guadix, Mr. Luis de Alarcón and Ariza.
The objective is that the seminarians have a place to relax. Fray Vicente Pontes y Cantelar, Bishop of Guadix between 1876 and 1893, focused his intellectual work on the San Torcuato Council Seminary, where he wanted to train priests with a broad intellectual and spiritual background, which is perfectly summed up in his educational motto “Science and fear of God”15. He was the one who carried out the transfer of the Seminary from its first location in the palace house of the Ramírez de Arellano in the cathedral square (today the School of Arts), to the old convent of San Agustín. A larger and more diaphanous building. It must have been something sentimentally dear, since it was the convent of the order from which he came. The official transfer took place on October 1, 1880 in a solemn ceremony16.
During the Civil War (1936-1939) the church of San Agustín, administered by the City Council and the UGT, served as a general store of provisions for the civil population. The building suffers a great deterioration to which must be added the collapse of the central dome. Don Rafael Álvarez Lara, Bishop of Guadix between 1943 and 1965, carried out a series of reforms in 1949. The floor plan of the building was transformed, endowing it with of a single rectangular main nave with a barrel vault over transverse arches and lunettes that illuminate the entire space. In 1952, the seminary was divided into “major” and “minor”, leaving the minor in the extinct convent of San Agustín and the major in a new building next to the Colegio Máximo de Cartuja in Granada, administered by the Compañía de Jesús19.
At the end of the 20th century, the building was definitively abandoned, yielding to the Hon. Guadix City Council, the seminary and the citadel in 1996, leaving the segregated church under the ownership of the Diocese of Guadix. Finally, the Diocese of Guadix, headed by its bishop Juan García Santacruz Ortiz, signs an agreement for the transfer of the temple of San Agustín in favor of the Very Illustrious and Fervent Brotherhood of Our Lady of Tears.