The Byzantine church, with central symmetry, was deeply rearranged by Counts Arcucci (the family of Charterhouse's founder) in the 14th century, who enlarged the church with a high presbytery covered with a cross vault on the Southern side, and with a porch and the current facade on the opposite side. In this way they changed the traditional sense of direction of the old Christian churches (from West to the East) to an unusual disposition from North to the South. They left inside some precious columns taken from the near Roman villa, which were instead removed in the 18th century, placed inside the Royal Palace of Caserta and replaced here with some poor copies.

In the wide area near the Church of San Costanzo had been placed the villa of Roman Emperor Octavian Augustus, the Sea Palace (that is also the name of the whole zone). Nowadays they remain only few ruins on the coastline, in a place called "Bagni di Tiberio" (Tiberius Baths), with a huge exedra and the pools for breeding fish, probably built or enlarged by Tiberius, as indicated by construction style. The nucleus of Augustus' villa was higher, in the place now occupied by the buildings of the ex-villa owned by Williams Bismark, also known as "Fortino" (Blockhouse) because it was erected upon the defences built by the French soldiers at the beginning of the 19th century, who used for militar purposes what it was left by the Bourbon archaeologists when they raped the imperial villa in the 18th century, stealing all the precious marbles, columns and decorations.