The monastery was established in the 16th century by two monks from the Kyiv Pechersk Lavra, Joel and Silvester, who settled in nearby caves.

Around 1612 or 1618 the owner of Zhovkva, Stanisław Żółkiewski offered the monks land to build their monastery, later surrounded with fortifications during the second half of the 17th century to defend it from roaming Tatar hordes.

In the 18th century the monastery's prosperity rose and wooden buildings were replaced with stone ones which stand there today.

With the collapse of the Soviet Union, the monastery was reopened on 29 August 1990 and the complex has undergone a thorough renovation.

The largest annual pilgrimage to Krekhiv is held on the Feast of the Translation of St. Nicholas on May 22 (May 9 according to the Julian calendar).