This monastery was founded by King Ferdinand II of Aragon and Queen Isabella I of Castile to commemorate both the birth of their son, Prince John, and their victory at the Battle of Toro (1476) over the army of Afonso V of Portugal.

[2][3] This apparent contradiction was a consequence of the indecisive[4][5] military outcome of the battle: the troops under Afonso V broke[6][7] while the forces led by Prince John of Portugal defeated[8][9] the Castilian right wing and remained in possession of the battlefield.

As summarized by the Spanish academic historian Rafael Casas: "...San Juan de los Reyes resulted from the royal will to build a monastery to commemorate the victory in a battle with an uncertain outcome but decisive, the one fought in Toro in 1476, which consolidated the union of the two most important Peninsular Kingdoms.

"[14] Toledo was chosen as the site for building the monastery due to its central geographic location and because it had been the capital of the ancient Visigoth kingdom, symbolically reconstituted by Isabella and Ferdinand with the restoration of the lost unity of Spain, through the union of Castile with Aragon.

The ground floor's ceiling is formed of German cross vaults set with figures of saints interspersed with animal and plant motifs, all created by the Toledo sculptor Cecilio Béjar in the 20th century.