The church was built on the site where the children from Alcalá, Justo and Pastor, were said to have been martyred. The original structure was an old collegiate church which was rebuilt by Cardinal Cisneros. It has three naves and an ambulatory. The central nave is covered with cross vaults, and the side naves with tiercerons. The doorway on the main façade is in the flamboyant Gothic style, with a low arch and a tympanum decorated with the crests of the church and of Cisneros, and an image of San Ildefonso. The incorrupt body of San Diego of Alcalá is on the high altar.