Christianity had lingered in Bavaria from Roman times; but a new era set in when Rupert, bishop of Worms, came to the country at the invitation of Duke Theodo I. in 696. He founded several monasteries, and a similar work was also performed by St Emmeran, bishop of Poitiers; with the result that before long the bulk of the people professed Christianity and relations were established between Bavaria and Rome. The 8th century witnessed indeed a heathen reaction; but it was checked by the arrival in Bavaria about 734 of St. Boniface, who organized the Bavarian church and founded or restored bishoprics at Salzburg, Freising, Regensburg and Passau.
Tassilo III., who became duke of the Bavarians in 749, recognized the supremacy of the Frankish king Pippin the Short in 757, but soon afterwards refused to furnish a contribution to the war in Aquitaine. Moreover, during the early years of the reign of Charlemagne, Tassilo gave decisions in ecclesiastical and civil causes in his own name, refused to appear in the assemblies of the Franks, and in general acted as an independent ruler. His position as possessor of the Alpine passes, as an ally of the Avars, and as son-in-law of the Lombard king Desiderius, was so serious a menace to the Frankish kingdom that Charlemagne determined to crush him. The details of this contest are obscure. Tassilo appears to have done homage in 781, and again in 787, probably owing to the presence of Frankish armies. But further trouble soon arose, and in 788 the duke was summoned to Ingelheim, where on a charge of treachery he was sentenced to death. He was, however, pardoned by the king; and he then entered a monastery and formally renounced his duchy at Frankfort in 794. The country was ruled by Gerold, a brother-in-law of Charlemagne, till his death in a battle with the Avars in 799, when its administration was entrusted to Frankish counts and assimilated with that of the rest of the Carolingian empire, while its condition was improved by the measures taken by Charlemagne for the intellectual progress and material welfare of his realm. The Bavarians offered no resistance to the change which thus abolished their dukedom; and their incorporation with the Frankish dominions, due mainly to the unifying influence of the church, was already so complete that Charlemagne did not find it necessary to issue more than two capitularies dealing especially with Bavarian affairs.