There are many indications that the villa was occupied for a long period, including the renovation of damaged mosaics and repairs to brickwork. Nevertheless, other clues, such as the limited presence of 4th- and 5th-century ceramics indicate that, after a remarkable transformation, a lengthy period of recession set in that led to the estate being abandoned.
The residential portion was modified, with the elimination of two of the trilobed room's secondary apses. Doors were closed up and others created, thus changing how one moved through the rooms. Gaps in worn mosaics were filled in with white tesserae or mortar, and the painted walls were repaired in order to keep a portion of the apartment in liveable condition. On the other hand, the original function of the room AA' was eliminated, with the removal of the marble panelling. A coating of tile-fragment cement was laid over the mosaics. This large space was turned into a utilitarian area, possibly a storeroom.
Lean-tos were added onto the facades as needed. The courtyard slowly lost its peristyle gallery and its garden role. New types of utilitarian constructions populated this open area, like a shed that was excavated. These transformations that affected the villa's appearance went hand-in-hand with new living conditions for its final occupants at the dawn of the Middle Ages.