We know from the preserved contract between the pastor Hostislav and Master Jan that it was explicitly stated that eight columns should be used to support sexpartite vaulting according to the pattern of the church of Sts.

Jiljí in Milevsko and the net vault inspired the cathedral of St. Vitus in Prague by Petr Parléř.

Although Master Jan Staněk, a member of the Prague Stonemason Family, started the construction, he did not continue to participate in it for unknown reasons.

Before 1500, an organ loft was built and another major intervention was the construction of a massive Rosenberg mausoleum and a new altar with the Rožmberk rider (coat of arms).

However, due to a lack of space after a severe plague, it was moved to today's City Park to St. Martin's Chapel.

On the north wall (to the left of the altar) is a valuable sanctuary from the year 1500 - made of stone, richly decorated.

The presbytery is segregated from the main nave by an ogive; only the upper arch seems vigorous, the ribs are more delicate alongside the canopies in which the sculptures are embedded.

The ribs pass through the walls without capitals turning into a rounded fine pillar that extends from the ground.

The Chapel of the Resurrection is originally Gothic, in the 18th century it was rebuilt in Baroque style (e.g. rid of ribs) and in 1777 it was painted by František Jakub Prokyš.

The two chapels are entered from the nave by semicircular arches.Almost the whole church masonry is covered in white plaster except the visible pier-butters extending from the south and the north walls, the corner masonry (for reinforcing the structure) and some minor decorations such as the window ledge lining the whole church.

The size of the tomb and its placement right in front of the altar had long been eyesore for the local Jesuits, who pointed out that the former ruler of the Dominicum had been compared to God.

The tomb was completely removed again in 1670, but it was totally expelled by Duke of Český Krumlov at that time, Jan Kristián I.

The pewter coffins of William and Anne of Baden were replaced with oaken ones and laid back in the underground cellar.

The above-ground part was dismantled, the columns were subsequently used to build a canopy for the baptistery, and the tombstones of William and Anne Mary were first set in front of the altar, then attached to the Chapel of Sts.

The last wish of Eleonora Amalia, the wife of the first Duke of Krumlov from the Schwarzenberg family, Prince Adam Francis, was to rest in the newly built Chapel of St. John of Nepomuk.