The decline of the Pechenegs is generally thought to start around 1036, although their unity faltered when in the late 10th and early 11th century Pechenegs were exposed to both Christanity and islam. In the first decade of 11th century, a religious divide occurred among thirteen Pecheneg tribes, with two of them, located in westernmost areas and governed by leader known as Kegen, accepted Christanity and subsequently accepted sovereignty of the Emperor Konstantinos IX and entered his service, settling in the area now roughly corresponding to Dobrudja. The remaining Pechenegs, under leader known as Tirakh, accepted islam.

In 1036 Yaroslav I, grand duke of Kievan Rus with his Polovets (Kuman) and Tork-Uz allies managed to defeat the Pechenegs and push them towards southwest, to the western shores of the Black Sea. In 1046-1047 the latter crossed the Danube and moved into Bulgaria, that was at the time governed by Byzantine Empire, entering conflict with this polity that will eventually lead to their ultimate defeat. It is worth noting that among the Byzantine troops opposing the invader are also Pechenegs who have entered Byzantine service earlier. Being pressured by Uzes from north-east, Pechenegs move into Balkans in 1051, and are later joined by Kumans and the Uzes themselves. In 1064 they manage to attack Thracia and move towards Constantinople, but as this land has been a part of the Eastern Roman Empire, they met with the retaliation from the Emperor Alexis I, also assisted by Kuman mercenaries. They posed a serious threat, but Byzantines manage to repel them 1087 at Dristra (now Silistra in Bulgaria), negotiate peace after Pechenegs almost reached Adrianople in 1089 and break siege of Maritsa in 1090 when invaders acted in cooperation with Seljuks.

The tide turns in 1091, when the Byzantine-Kuman army surprises the main Pecheneg forces at Lebounion. The army, moving along their families, has been almost completely annihilated. Although Anne Komnene, said that the 'entire nation, tens of thousands strong, with its women and children, ceased to exist on that day', it is now considered a substantial exaggeration. Substantial number of survivors were brought back to Empire as prisoners after the battle, and it is known that some part of the survivors has been recruited by the victorious Emperor who then settled them in region of Moglena, captured by Basil II several decades before. It is also understood that not all Western Pechenegs took part in the Battle of Levounion, as there were other battles between Pecheneg and Kuman groups in the area throughout early 1090s. Other groups were also living on the Pontic Steppes and were eventually expelled by Vladimir II in 1121, after which they moved southwest, entering the Byzantine territory. This again caused retaliation from the Emperor Ioannes II who defeated them in the battle of Beroia (now Stara Zagora in Bulgaria) in 1122. This event largely marks the end of Pecheneg threat, as the remaining groups were too small and scattered, eventually being assimilated by the local peoples, mainly Hungarians, Bulgarians and Greeks.

Some historians support the idea that direct descendants of Pechenegs are Gagauzes who inhabit the Gagausia in what is now Moldova and also live in small communities in Bulgaria, Romania and Kazakhstan. It is also suggested that some of the Pechenegs joined Caucasian Bashkir and Kyrgyz clans (some point to the Kyrgyz Bechen clan that is allegedly Pecheneg in origin, although it might be simply an onomastic coincidence). Substantial number of Pechenegs, as well as the Torks and Barendeys have been also settled by Kievan rulers in the southern reaches of their lands in 11th and 12th century. Some Pechenegs were also settled in Hungary in 11th and 12th century, mainly in the regions Fejer and Tolna.

So, after the series of defeats at the hands of Byzantines in late 11th and early 12th century century, the Pechenegs ceased to exist as a large, unified group and were rendered into disjointed communities that were ultimately absorbed and assimilated into the other cultures, primarily in what is now the Balkan regions and Kazakhstan.