The first Jesuit school in Arequipa was founded in 1578 under the name Colegio de Santiago but was soon closed by Viceroy Francisco de Toledo, who opposed the school.
Following the signing of peace, Álvarez de Toledo returned to Spain and later went to Ghent, in Flanders.
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He was a direct descendant of the earlier Túpac Amaru, the last Inca (Emperor) of Vilcabamba, who had been beheaded on the orders of Viceroy Francisco de Toledo in 1572.