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The gradual decline of Avar power accelerated to a rapid fall. A series of Frankish campaigns, beginning from 788, ended with the conquest of the Avar realm within a decade. Initial conflict between Avars and Franks occurred soon after the Frankish deposition of Bavarian duke Tassilo III and the establishment of direct Frankish rule over Bavaria in 788. At that time, the border between Bavarians and Avars was situated on the river Enns. An initial Avarian incursion into Bavaria was repelled, and Franco-Bavarian forces responded by taking the war to neighbouring Avarian territories, situated along the Danube, east of Enns. The two sides collided near the river Ybbs, on Ybbs Field (German: Ybbsfeld), where the Avars suffered a defeat in 788. This heralded the rise of Frankish power and Avarian decline in the region.

In 790, the Avars tried to negotiate a peace settlement with the Franks, but no agreement was reached. A Frankish campaign against the Avars, initiated in 791, ended successfully for the Franks. A large Frankish army, led by Charlemagne, crossed from Bavaria into the Avarian territory beyond the Enns, and started to advance along the Danube in two columns, but found no resistance and soon reached the region of the Vienna Woods, near the Pannonian Plain. No pitched battle was fought, since the Avars had fled before the advancing Carolingian army, while disease left most of the Avar horses dead. Tribal infighting began, showing the weakness of the khaganate.

The Franks had been supported by the Slavs, who established polities on former Avar territory. Charlemagne's son Pepin of Italy captured a large, fortified encampment known as "the Ring", which contained much of the spoils from earlier Avar campaigns. The campaign against the Avars again gathered momentum. By 796, the Avar chieftains had surrendered and became open to the acceptance of Christianity. In the meantime, all of Pannonia was conquered. According to the Annales Regni Francorum, the Avars began to submit to the Franks in 796. The song " De Pippini regis Victoria Avarica " celebrating the defeat of the Avars at the hands of Pepin of Italy in 796 still survives. The Franks baptized many Avars and integrated them into the Frankish Empire. In 799, some Avars revolted.

In 804, Bulgaria conquered the southeastern Avar lands in Transylvania and southeastern Pannonia up to the Middle Danube, and many Avars became subjects of the Bulgarian Empire. Khagan Theodorus, a convert to Christianity, died after asking Charlemagne for help in 805; he was succeeded by Khagan Abraham, who was baptized as the new Frankish client (and should not be assumed from his name alone to have been Khavar rather than Pseudo-Avar). Abraham was succeeded by Khagan (or Tudun) Isaac (Latin Canizauci), about whom little is known. The Franks turned the Avar lands under their control into a frontier march. The March of Pannonia — the eastern half of the Avar March — was then granted to the Slavic Prince Pribina, who established the Lower Pannonia principality in 840.

Whatever was left of Avar power was effectively ended when the Bulgars expanded their territory into the central and eastern portions of traditional Avar lands around 829. According to Pohl, an Avar presence in Pannonia is certain in 871, but thereafter the name is no longer used by chroniclers. Pohl wrote, "It simply proved impossible to keep up an Avar identity after Avar institutions and the high claims of their tradition had failed", although Regino wrote about them in 889. The growing amount of archaeological evidence in Transdanubia also presumes an Avar population in the Carpathian Basin in the late 9th century. Archaeological findings suggest a substantial, late Avar presence on the Great Hungarian Plain; however, it is difficult to determine their proper chronology. The preliminary results of the new excavations also imply that the known and largely accepted theory of the destruction of the Avar settlement area is outdated; a disastrous depopulation of the Avar Khaganate never happened.

Byzantine records, including the " Notitia episcopatuum ", the " Additio patriarchicorum thronorum " by Neilos Doxapatres, the " Chronica " by Petrus Alexandrinus and the " Notitia patriarchatuum " mention the 9th century Avars as an existing Christian population. The Avars had already been mixing with the more numerous Slavs for generations, and they later came under the rule of external polities, such as the Franks, Bulgaria, and Great Moravia. Fine presumes that Avar descendants who survived the Hungarian Conquest in the 890s were likely absorbed by the Hungarian population. After the mid to late 8th-century Frankish conquest of Pannonia, Avar and Bulgar refugees migrated to settle in the area of Bulgaria and along its western periphery. The Avars in the region known as solitudo avarorum — currently called the Great Hungarian Plain — vanished in an arc of three generations. They slowly merged with the Slavs to create a bilingual Turkic-Slavic-speaking people who were subjected to Frankish domination; the invading Magyars found this composite people in the late 9th century. The De Administrando Imperio, written around 950 and based on older documents, states that "there are still descendants of the Avars in Croatia, and are recognized as Avars". Modern historians and archaeologists until now proved the opposite, that Avars never lived in Dalmatia proper (including Lika), that statement occurred somewhere in Pannonia, and the information belongs to the 9th century. There has been speculation that the modern Avar people of the Caucasus might have an uncertain connection to the historical Avars, but direct descent from them is rejected or doubted by many scholars.