According to a later legend, the monastery was founded around 1330 by the Tatar nobleman Chet, who, fleeing from the Golden Horde to Ivan Kalita, was baptized in Moscow under the name Zachariah. The Mother of God appeared to him here with the apostle Philip and the holy martyr Ipatiy of Gangra, which led to his healing. In gratitude, he founded the monastery. Modern researchers consider nobleman Chet to be a mythical figure, and the "Tale of Prince Chet" a genealogical legend created to give princely status to the Godunov family. Historian Stepan Veselovsky attributed the founding of the monastery to the end of the 13th century. Initially, the Church of the Holy Trinity was built, followed by the Church of the Nativity of the Virgin, several cells, and an oak wall. Surrounding it were residential and economic buildings, all made of wood. According to one version, the monastery was founded by Prince Vasily Yaroslavich, the brother of Alexander Nevsky, who preferred to live in Kostroma. The deeds of Vasily Yaroslavich are also attributed to the legendary Prince Vasily Kvashnya. According to another version, the monastery was founded by Novgorodians, as Saint Ipatiy was the patron of the posadniks of Novgorod, and the Kostroma River served as a route to the Volga. After the death of Prince Vasily and the abolition of the Kostroma principality, the monastery came under the protection of the Godunov family, which rose to prominence in the 16th century. The Godunovs considered Zachariah their ancestor and became the patrons of the monastery. It houses the family burial site, including the graves of Boris Godunov's parents. During this period, the monastery actively developed. From 1586 to 1591, it received 1000 rubles and several villages from the Godunovs. By 1600, the monastery became the fourth largest landowner in Russia, owning more than 400 villages. With the funds of Dmitry Godunov, stone walls with towers were erected, and the Trinity Cathedral was laid. In 1564, the construction of the winter church of the Nativity of the Most Holy Theotokos was completed. In 1595 and 1597, a church was built over the Holy Gates. The Godunovs donated numerous church books and utensils. A painting workshop and a large library were established in the monastery. Thanks to the efforts of the Godunovs, by the end of the 16th century, the monastery gained significance in the political and spiritual life of Rus. It was called the "Renowned Lavra," and in 1599, the abbot was granted the rank of archimandrite.

During the Time of Troubles, the monastery experienced decline. After Tsar Vasily Shuisky appealed for help, Archimandrite Theodosius and Igumen Arseny went to Tushino in 1608 and swore allegiance to False Dmitry II. The monastery fell into the hands of his supporters. In February 1609, the people of Kostroma rebelled but could not immediately take the monastery, protected by strong walls and cannons. In April, Vasily Shuisky's army began the siege, and only in September 1609 was the monastery captured. From the autumn of 1612, the young Mikhail Romanov and his mother lived here. On March 13, 1613, a delegation from the Zemsky Sobor arrived at the monastery, which elected Mikhail as tsar. On March 14, a ceremony was held in the Trinity Cathedral to summon Mikhail Romanov to the throne, which marked the end of the Time of Troubles.

On November 23, 1989, the first service was held after the monastery's closure, and in 1991, the Holy Trinity Ipatiev Monastic Community was registered. In 1993, despite protests, the community was given the territory of the New Town. In 2002, due to negligence, the Church of the Transfiguration of the Savior built in 1628 burned down. In 2004, by order of the President of Russia, the buildings of the monastery were transferred to the Kostroma Diocese. This caused discontent, as the museum-reserve was left without premises. The archimandrite of the monastery is Bishop Ferapont of Kashin, and his deputy is Hieromonk Peter Yeryshalov.