The church of St. Agnes belongs to the same early Byzantine period as the church of St. Andrew. You can conclude from the remnants that it had the function of a burial church, as there are some graves in the surrounding area. The church was discovered in 2005, during the excavation of drywall covered in construction waste material, although the location was previously known as St. Agnes.
The church was built on an existing mausoleum from the 2nd century, although the church itself dates back to the 5th century. The building has four strong buttresses on the eastern side, while on the western side, a few steps can be found. A thinner circular wall was situated on the northern side for food storage that got destroyed during WWII in the process of constructing a bunker. All of the excavated walls are preserved.