The church Assumption of Virgin Mary was built as a double nave with rectangular polygonal choir situated in the north nave. The complex of the monastery building is attached to its northern part. In baroque times the central chapel Jesus Christ Crucifixion and Grievous Virgin Mary was built additionally and connected with the southern wall. The chancel and the double nave were provided with supporting pillars which can be seen only by the north nave in the cross-shaped corridor. The choir is arched in a rib-vault with terracotta groins running out from pyramidal console and intersecting in target-like bolts with signs. By the year 1500 the double nave had had diamond vault borne by three polygonal pillars with octangle bases. That type of rib-less vaulting can be found in other parts of the monastery, it represents the biggest complex of diamond vaulting in the Czech Republic. A baroque choir loft was built in the western part of the nave in 1634 which caused the destruction of the late gothic painting of the Great Tribulation on the western wall; the painting was discovered in 1943 and then restored.

The monastery became an important pilgrimage place after the Thirty Year War; three miraculous sculptures rescued after the monastery demolition in the beginning of the mentioned war were worshiped. The last Franciscans were violently deported from Bechyně in 1950.