In July of 1593, the Cardinal travels to Madrid where he visits the Jesuits' provincial to make the foundation and endowment of the School official and in writing. In this document, there is mention of the transfer of a set of relics to the institution.
The construction suffered many interruptions. Master builder Diego de Isla was expelled, and the work on the church was halted after the death of Juan de Cajigas. In 1598, Rodrigo de Castro gives authority to the Countess of Lemos, Catalina de Zuñiga, to resume the projects. Juan de Tolosa is named master builder, mainly of the house and schools. In 1598, Diego de Vélez and Gonzalo de Güemes join the projects under the supervision of Juan de Tolosa, Jesuit architect, disciple of Juan de Herrera. In 1600, also Jesuit, Juan Bustamante was made principle master builder of the construction. Nevertheless, upon the death of the Cardinal in this same year, the work is interrupted for several years. Simón de Monasterio finished the church and in 1619, the shrine is consecrated as totally completed.
As a whole, it is a Mannerist complex, arranged with two cloisters at the sides of the “Vignolesco” shrine covered with a dome, recalling in its grandeur, the Escorial.


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