The Templar order was suppressed throughout most of Europe from 1312–1314, but in Portugal its members, assets, and partly its membership were transmitted to the Order of Christ, created in 1319 by King Dinis. The Order of Christ moved to Tomar in 1357, which became its headquarters.

One of the most important Grand Masters of the Order was Prince Henry the Navigator, who ruled the Order from 1417 up to his death in 1460. Prince Henry gave great impulse to the pioneering Portuguese expeditions during the Age of Exploration. In the Convent, Prince Henry ordered the construction of various cloisters and other buildings. He also sponsored urban improvements in the town of Tomar itself.

Another important personality related to the Order was King Manuel I, who became Master of the Order in 1484 and King of Portugal in 1492. Under his reign there were several important improvements in the Convent, specially the addition of a new nave to the round church and its inner decoration with paintings and sculptures.

The successor of Manuel I, King John III, demilitarised the order, turning it into a more religious order with a rule based on that of Bernard of Clairvaux. He also ordered the construction of a new cloister in 1557, which is one of the best examples of Renaissance architecture in Portugal.

In 1581, after a succession crisis, the Portuguese Nobility gathered in the Convent of Christ in Tomar and officially recognised Philip II of Spain (Philip I of Portugal) as King. This is the beginning of the Iberian Union (1581–1640), during which the Crowns of Portugal and Spain were united in a dynastic union. The aqueduct of the Convent was built during this period.