The Byzantines ruled Bulgaria from 1018 to 1186, subordinating the independent Bulgarian Orthodox Church to the authority of the Ecumenical Patriarch in Constantinople but otherwise interfering little in Bulgarian local affairs. There were rebellions against Byzantine rule in 1040-41, the 1070s and the 1080s, but these failed. By the late 12th century the Byzantines were in decline after a series of wars with the Hungarians and the Serbs. In 1185 Peter Asen, a leading noble of mixed, Cuman-Bulgarian origin, led a Bulgarian revolt against Byzantine rule and declared himself Tsar Peter II (also known as Theodore Peter). The following year the Byzantines were forced to recognise Bulgaria's independence. Peter styled himself "Tsar of the Bulgars, Greeks and Vlachs.

Resurrected Bulgaria initially occupied borders very similar to those of modern Bulgaria, since the power of the Serbs, Hungarians and Cumans prevented any expansion to the north. Under Ivan II, however, Bulgaria once again became a regional power, occupying Belgrade and Albania. Ivan had a reputation as a wise and humane ruler, and opened relations with the Catholic west, especially Venice and Genoa, to reduce the influence of the Byzantines over his country.

Frescoes from the Boyana Church (1259): DesislavaIn the 13th and 14th centuries Bulgaria became a thriving cultural centre. The flowering of the Turnovo school of art was related to the construction of palaces and churches, to literary activity in the royal court and the monasteries, and to the development of handicrafts. Remarkable achievements of this school have been preserved down to this day: the murals of the Boyars' houses in Trapezitsa and the Forty Holy Martyrs church in Veliko Tarnovo, the Boyana Church (1259) and the Rock-hewn Churches of Ivanovo. Book illuminations also developed, examples include the Manasses Chronicle, the Tetraevangelia of Ivan Alexander and the Tomich Psalter.

But under Ivan II's successors, Bulgaria once again declined. When Constantinople fell to the Fourth Crusade in 1204, Bulgaria was forced to cede Macedonia to the Latin Empire. The Mongols also raided the Balkans in the early 13th century, devastating Bulgaria in 1242, and Bulgaria was forced to pay tribute to the Khans of the Golden Horde. By the reign of Ivan III 1279-1280, Bulgaria was reduced to a small state on the south bank of the Danube.

The withdrawal of the Mongols from Europe in the early 14th century stabilised the situation in the Balkans and Bulgaria reassumed something like its modern borders. But Bulgaria was threatened by the rising powers of Hungary to the north and Serbia to the west. In 1330 the Bulgarians under Michael III were heavily defeated by the Serbs at Velbuzhd, and large parts of Bulgaria came under Serbian domination. Under Ivan IV (Ivan Alexander) Serbian control was ended, but Bulgaria was left divided into rival states; of the two largest, one was based at Veliko Turnovo and the other at Vidin, ruled by Ivan's two sons.

Weakened Bulgaria was thus no match for a new threat to the south, the Ottoman Turks, who crossed into Europe in 1354. In 1362 they captured Philippopolis (Plovdiv), and in 1382 they took Sofia. The Ottomans then turned their attentions to the Serbs, whom they routed at Kosovo Polje in 1389. This battle sealed the fate of the Balkans for 500 years. In 1393 the Ottomans occupied Veliko Turnovo after a three-month siege. In 1396 the Despotate of Vidin was also occupied, bringing the Second Bulgarian Empire and Bulgarian independence to an end.