The church was constructed by the Knights Hospitaller when the order settled in Santarém after the foundation of the Kingdom of Portugal, in the 12th century. Although other orders settled in the Kingdom after the Reconquista.

The Knight Hospitaller built the church after the city was conquered to the Moors. Besides the church been changing through the time, it is known that there was a featured tower in the building.

The church has lost its importance throughout the years, being used as a warehouse for a certain period. Nevertheless, the sense of depth and mystery never left this church, which is now available for visits, to let people know a bit more about these orders. The church also has a museum, where visitors may learn about its history in more detail.

The church is dedicated to Saint John the Baptist, showcasing the importance of Baptists to this order.