St. Thomas church was constructed by the Benedictines along with the chapel of St. Dorothy in 1228. In 1285 when Vaclav II was in power, a new Order called Ordo eremitarum sancti Augustini (Order of St. Augustine’s Hermits) settled in the church on the king’s invitation.

The biggest reconstruction of the monastery area began in 1550 and was completed during the 30-year war. In the Rudolfine age, the monastery became an important spiritual centre for all catholic members of the empire. During the 18th century, the church and the convent gained the appearance they have today. A remarkable architecture complex was built encompassing three constructional stages in a quite organic way: Gothic, Renaissance and Baroque.

As was the case with other monasteries in 1950, even the friars of St. Thomas were forced to end their monastery lives. They were evicted and the convent was turned into a retirement home. The revitalization in the 70s was only aimed at the church. After 1990, the last large repair was done including a replacement of the truss, which was infected by the woodworms.