In 80 CE the Great Fire in the Campus Martius badly damaged the Theater of Balbus, as well as the Theater of Pompey and many other monuments which Dio Cassius (c. 220 CE) ennumerates (Roman Histories 66.24.1-3).
Domitian (81-96) undertook a major renovation of the Campus Martius which probably included the Balbus complex, for closure of the niches in the external facade, datable to this period, indicate that the crypta at least was already assigned to other functions (possibly as the headquarters of the vigiles).
Under Hadrian (117-138), the portico of the crypta was again modified, with the exedra converted into a huge latrine.
Evidence for the continued existence of the Balbus complex in the age of Constantine is provided by the 4th Century Notitia Regionum XIV, which describes noteworthy objects in the fourteen regions of Rome. The list for Regio IX contains entries for each of the three theaters of the Campus Martius, as well as an entry for "Cripta Balbi."
In late antiquity repeated violent floods of the Tiber, sacks of Rome, damaging earthquakes, fires, and private use took their toll of the complex. The emperor Theodoric undertook the final restoration of the crypta in 507-511.
Of the subsequent phases of the site which the Crypta Balbi museum publication documents, Daniele Manacorda writes in her introduction : "The excavations soon revealed that life had continued on the site of the Crypta Balbi after antiquity. A continuous sequence of transformation and reuse of the monument ran through the Middle Ages and the Renaissance until the modern era" (Museo Nazionale Romano Crypta Balbi, produced by the Ministero per i Beni e la Attivita Culturali (Milano: Electa, 2000, p. 5).
Between the 7th-9th century the exedra was used as a glass factory, a trash dump, and a lime factory, where ancient materials from the Balbus site and from all over Rome were reduced. During the Middle Ages a church was built over the temple-like structure in the center of the crypta and the theater served as a foundation for a large building, the Castrum Aureum.
For results of the massive archaeological excavation of the Theater and Crypta of Balbus undertaken by the Soprintendenza Archeologica di Roma, see the exhibit catalogue (the source of much material posted here) and the on-line announcement of the April 2, 2000, opening of the Crypta Balbi Museum on the original site. Additional images of the Theater of Balbus can be seen on-line at Civilta Museum.