The tribes who pushed into the territory of the present Diocese of Brixen, during the great migratory movements, especially the Bavarians and Lombards, accepted Christianity at an early date; only the Slavs of the Puster Valley persisted in paganism until the 8th century.

The diocese received many grants from the Holy Roman Emperors: thus from Conrad II in 1027 the suzerainty in the Norital, from Henry IV in 1091 the Puster Valley.

Likewise Duke Frederick IV of Habsburg, ruler of Tyrol and Further Austria, called "of the Empty Pockets", compelled the Bishops of Brixen to acknowledge his authority.

The Reformation was proclaimed in the Diocese of Brixen during the episcopate of Christoph I von Schrofenstein (1509-1521) by German emissaries, like Strauss, Urban Regius, and others.

Bishops of the period include: Cardinal Andrew of Austria (1591-1600), and Christoph IV von Spaur (1601-1613), who in 1607 founded a seminary for theological students; enlarged the cathedral school, and distinguished himself as a great benefactor of the poor and sick.

The most prominent prince-bishops of this period were: Kaspar Ignaz, Count von Kunigl (1702–47), who founded many benefices for the care of souls, made diocesan visitations, kept a strict watch over the discipline and moral purity of his clergy, introduced missions under Jesuit Fathers, etc.

The Government of Emperor Joseph II dealt roughly with church interests; about twenty monasteries of the diocese were suppressed, a general seminary was opened at Innsbruck, and pilgrimages and processions were forbidden.

During the brief rule of Bavaria after the 1805 Peace of Pressburg, the greatest despotism was exercised towards the Church; the restoration of Austrian supremacy in 1814 improved conditions for the former bishopric territory.