The monastery was founded in 1083 by Prince Gregory Pakourianos, a prominent statesman and military commander in the Byzantine service, as a Georgian-dominated Orthodox monastery.[1] He set up a seminary(school) for the youth at the monastery. The curriculum included religion, as well as mathematics, history and music. In the 13th century, the Georgian and Chalcedonic Armenian monks[2] of the Petritsioni (Bachkovo) Monastery lost their domination over the monastery, but their traditions were preserved until the beginning of 14th century and an Armenian Gospel from the 10th century that came from this monastery still exists today.[3] During the time of the Second Bulgarian Empire, Bachkovo Monastery was patronized by Tsar Ivan Alexander, which is evidenced by an image of him on the arches of the ossuary's narthex. It is believed that the founder of Tarnovo Literary School and last patriarch of the mediaeval Bulgarian Orthodox Church, Patriarch Euthymius, was exiled by the Turks and worked in the school of the monastery in the early 15th century.

Although the monastery survived the first waves of Turkish invasion in Bulgarian lands, it was then looted and destroyed, but restored near the end of the 15th century. The refectory, whose mural paintings by an anonymous painter bear a significant artistic value, was reconstructed in 1601 and the Church of Mary, still preserved today, was finished in 1604.

Bachkovo Monastery is the final resting place of both Patriarch Euthymius (1330–1404) and Patriarch Cyril (1953–1971).