By the beginning of the 18th century, the Holy Trinity Monastery was in a state of neglect. Metropolitan Philotheus, showing particular care for the monastery, decided to restore it and make it more majestic. There were few exiles in Tyumen, especially stonemasons, only six in total, four of whom were building the Annunciation Cathedral. Therefore, local residents were involved in the construction of the church.

On June 12, 1709, Emperor Peter I ordered the allocation of one thousand rubles from the Tobolsk treasury for the construction of the church, not including sheet iron for the roof. Thanks to these funds, it became possible to hire workers. Governor Prince Gagarin also assisted the metropolitan by sending stonemasons and bricklayers from Verkhoturye and Solikamsk, as well as blacksmiths and carpenters.

In the seventh year of his stay in Siberia, Metropolitan Philotheus fell seriously ill. In 1709, he took monastic vows with the name Theodor and retired to the Holy Trinity Monastery. Until the arrival of the Tobolsk Metropolitan Ioann Maximovich on August 14, 1711, Philotheus managed the diocese from the monastery. Schema-monk Theodor continued to oversee the construction of the cathedral. Despite Peter I's decree of December 9, 1714, prohibiting stone construction in cities, except for St. Petersburg, work at the Tyumen monastery continued. The names and locations of the altars changed, but the central part, the Trinity, remained as envisioned by Saint Philotheus.

The cathedral was completed in 1715, and Schema-monk Theodor requested a blessing from Saint Ioann for its consecration. The blessing was received, and the cathedral was consecrated on June 3/16, 1715. The two-story, five-domed Trinity Cathedral became a true gem of the monastery. Inside, the temple was adorned with magnificent iconostases, shining with gold and bright colors. The icons were painted by monk masters invited from Kyiv. The first iconostasis served for one and a half centuries. The Transfiguration chapel also had a beautiful iconostasis, preserved until the 1920s. No data on the wall paintings of the cathedral have survived.

The Holy Trinity Cathedral was closed on August 11, 1923. Despite the changes, former parishioners hoped for the resumption of services. In 1925, they created a community of the Holy Trinity Cathedral, but requests for conducting services and transferring church utensils were denied. After 1927, no attempts were made to revive the prayer life.

On February 22, 1995, the Holy Synod decided to revive the Holy Trinity Monastery. On September 2, 1995, bishops Vasily Rodzyanko and Dmitry visited the cathedral, expressing confidence in its revival. On March 7, 1996, an assessment of the cathedral's condition was made, indicating the need for significant repair work.

On December 10, 1996, the cathedral was handed over to the Tobolsk-Tyumen Diocese. The first service in the Assumption chapel took place on August 28, 2001, after which they became regular.

On November 16, 2001, the governor of Tyumen region S.S. Sobyanin visited the cathedral and promised assistance in its restoration. In 2002, work began in the main chapel, and on November 29, 2002, the installation of the iconostasis commenced. On March 17, 2003, work on its installation continued.

On June 15, 2003, Archbishop Dmitry conducted the first service in the cathedral in 80 years. On November 28, 2005, new gilded domes were installed.

In February 2014, the cathedral was closed for major restoration.