The Dominican Monastery of Santo Tomás was built under the patronage of Hernando Núñez de Arnalte (treasurer of the Catholic Monarchs), his wife, María Dávila, the Inquisitor Fray Tomás de Torquemada and the Catholic Monarchs. The work began in 1482 and was completed in 1493; however, at the Catholic Monarchs' initiative, a palace was built around the eastern cloister or the cloister 'of the Monarchs', together with the sepulchre of Prince Juan in the church after he had died in 1497.
As a see for the Inquisition, the University of Santo Tomás was opened in the 16th century and remained in operation until the 19th century. The monastery has been attacked many times throughout its history: sacked during the French invasion, abandoned after the sale of church lands ordered by Mendizábal and destroyed by fires in 1699 and 1936.
The complex has three cloisters:
- The Novices' Cloister. This is of Tuscan style and has 20 arches; it has a particularly sober appearance and has no decoration whatsoever.
- The Cloister of Silence or the Deceased. Here is where the monks were buried; it has 18 arches on the ground floor and 38 polylobate arches on the upper floor, with a large amount of decoration on the intermediate sections.
- The Cloister of the Monarchs. This cloister distributes the areas in the Royal Palace. It has 40 arches on the ground floor and 56 on the upper floor, decorated with typical Ávila beading.
The church front is based on a segmental arch and two buttresses that run through the arch vertically. The subtlety is broken by the existence of a huge rose window and the no less imposing coat of arms of the Catholic Monarchs. The decoration is completed with 10 sculptures by Gil de Siloé.
The interior stands out thanks to the elegance of the main nave and the ramifications of the ribs that make up the vault above the transept, marking off the area dedicated to the sepulchre of Prince Juan.
The palace is used as an Oriental Art Museum and a Natural Science Museum.
It was designated a National Monument in 1931.