Tal como sucedió en el Convento Santo Domingo, y en muchas otras iglesias en Buenos Aires, en 1955 fue saqueada y algunas de sus imágenes originales quemadas y perdidas.
Between the years 1775 and 1791, the church took over as the Cathedral of Buenos Aires, due to renovation work which was being done to the Cathedral.
Beside the church, the order of the Jesuits, built a school (Colegio San Ignacio), which after the order of the Jesuits were expelled by order of King Charles III in 1767, the school was renamed as the Real Colegio San Carlos, and is known since 1863 as the Colegio Nacional Buenos Aires. Probably one of the most prestigious public schools in the counrty. In 1821 the church is used as the venue in which the opening act of the Buenos Aires University takes place.
As it occured with the Santo Domingo Convent, and many other churches in Buenos Aires, it was sacked and burnt in the distrubances of 1955, and some of its original art work was lost to the flames.