The monastery was founded in the 16th century by two monks from the Kiev Pechersk Lavra, Joel and Silvester, who settled in nearby caves. Around 1612 or 1618, the owner of Zhovkva, Stanisław Żółkiewski, offered the monks land for the construction of their monastery, which was surrounded by fortifications in the second half of the 17th century to protect it from the invading Tatar hordes.
The hardest time for Krekhiv came with the beginning of the Soviet occupation in 1939; In 1949 the monastery was closed and many of the monks were tortured in Soviet prisons while others had to live in hiding. After the collapse of the Soviet Union, the monastery reopened on August 29, 1990, and the complex underwent a thorough renovation.