According to the legal sources of the time, these territories constituted the so-called Provincia Italiae, on the basis of the fact that they too, until at least the end of the 7th century, fell under the jurisdiction of the exarch and were governed by duces or magistri militum under him.

The necessities of war pushed military commanders to centralize powers, thus depriving the civil authorities which are no longer attested by sources starting from the second half of the 7th century.

Starting from the second half of the 7th century, the autonomist tendencies of the local aristocracies and the ever-increasing temporal political role of the Church of Rome led to a progressive weakening of imperial authority in Italy.

Byzantine Italy had now fragmented into a series of autonomous duchies outside the effective control of the exarch, whose authority no longer extended beyond the Ravenna area.

The armies, recruited from the local population, tended to take the pontiff's defense, and did not hesitate to turn on the exarch if he plotted against the Papacy.

In 476 Ravenna fell due to a military coup d'état by the general Odoacer who, at the head of a militia of Heruli, Sciri, Rugii and Turcilingi mercenaries (i.e. the Germanic component of the imperial troops), ousted Romulus Augustulus and took possession of the city.

On 13 August 554, with the promulgation in Constantinople by Justinian of a pragmatica sanctio pro petitione Vigilii (pragmatic sanction on the requests of Pope Vigilius), the Prefecture of Italy returned, although not yet completely pacified, to Roman dominion.

Consequently, at the end of the conflict, the prefecture of Italy, also called Provincia Italiae by the Pragmatic Sanction as if to demonstrate a loss of importance, was reduced to only continental and peninsular Italy (Sardinia and Corsica, conquered by the Vandals in the century, after Justinian's reconquest they became part of the Praetorian prefecture of Africa).

Four military commands were allocated to defend the prefecture, one in Forum Iulii, one in Trento, one in the region of Lake Maggiore and Como and finally one in the Cottian and Graian Alps.

Other military initiatives led by Faroald and Zotto, penetrated into Central and Southern Italy, where they established the duchies of Spoleto and Benevento.

In 580, Emperor Tiberius II reorganized them into five province eparchies: the Annonaria in northeastern Italy around Ravenna, Calabria, Campania, Aemilia and the Urbicaria around the city of Rome (Urbs).

The title of the Doge of Venice included the phrase dux Veneciarum provinciae, marking it as a province of the Byzantine Empire.

Ravenna, governed by its exarch, who held civil and military authority in addition to his ecclesiastical office, was confined to the city, its port and environs as far north as the Po (bordering territory of the duke of Venice, nominally in imperial service) and south to the Marecchia River, beyond which lay the Duchy of the Pentapolis on the Adriatic, also under a duke nominally representing the Emperor of the East.

In its internal history, the exarchate was subject to the splintering influences that were leading to the subdivision of sovereignty and the establishment of feudalism throughout Europe.

During the 6th and 7th centuries, the growing menace of the Lombards and the Franks, as well as the split between Eastern and Western Christendom inspired both by iconoclastic emperors and medieval developments in Latin theology and culminating in the acrimonious rivalry between the Pope of Rome and the Patriarch of Constantinople, made the position of the exarch more and more untenable.

The southern portions of the exarchate including the imperial possessions at Naples, Calabria, and Apulia were reorganized as the Catepanate of Italy headquartered in Bari.