The monastery was founded in 1627 as a defensive one. The founders of the monastery and the church of the Bernardine monks were the princes of Zbarazh. The Bernardines appeared near Zbarazh in 1627 at the invitation of Prince Jerzy Zbarazhsky, castellan of Krakow. He built a wooden monastery for them and began the construction of a stone church and monastery.
The construction of the church began in 1627 and was completed 10 years later by the efforts of Prince Janusz Vyshnevetsky and his wife Eugenia. In 1637, Princess Vishnevetskaya signed the act of founding the monastery. During the Cossack wars, the monastery survived, although it was badly damaged. In 1675, the Tatar and Turkish conquerors destroyed the church and the monastery, and only in 1723, with the help of Jozef and Stanislav Potocki, the majestic church of St. Anthony, which has survived to this day. The consecration took place on August 2, 1755. In 1755 the monastery was reconstructed in the Renaissance-Baroque style. The so-called "illusory painting" was applied in the interiors. Partially preserved altars with sculptural decoration of the XVIII century. (Authorship of A. Osinsky), fragments of murals of the end of the 18th century. and XIX Art. Only fragments have survived from the painting, as well as from the wonderful carved decor of the monastery. The monastery was one of the most influential in Podolia until the Austro-Hungarian times (1785), when the institution was "secularized" by order of the Caesar. Philosophical studios operated under the monastery, and provincial chapters took place. Since 1768, a hospital-asylum for the poor and sick operated at the monastery, and since 1777, a parish school and a Latin gymnasium. Ignacy Dashinsky (politician, prime minister of the Lubelsk government in 1918) and archbishop Ignacy Tokarczuk, holder of the Order of the White Eagle, were educated here.
During the Ukrainian-Polish war of 1918-1920. the monastery was badly damaged, and already in the post-war period it turned into ruins. The bell tower (1746-1755, architect Johann Ganz) is part of the Bernardine monastery complex. Unlike the church, the bell tower was not damaged during the fire in 1788, and therefore retained its original baroque forms.

The Bernardines returned to the city in 1990. At the moment, the temple is gradually being brought back to normal, although its cellars are said to be still full of bones and skulls - either these are "souvenirs" from the monks of past centuries, or from later victims of totalitarian regimes, to say hard.