The main Nikolsky temple of the monastery became cramped due to the increasing number of monks and parishioners. Therefore, the abbot Archimandrite Athanasius, along with the brotherhood, appealed to Bishop Justin of Perm and Yekaterinburg with a request to allow the construction of a second stone church. The Perm Spiritual Consistory granted permission on August 3, 1821, for the erection of a large stone church in the name of the Transfiguration of the Lord, with two chapels: in honor of the Annunciation of the Most Holy Theotokos and the Archangel Michael, as well as a bell tower. The laying of the church took place on August 28, 1821, and on August 30, 1834, the main Transfiguration temple was consecrated by Archbishop Arkady of Perm and Verkhoturye. The chapels were consecrated by him on July 25, 1837.

Behind the main choir of the Transfiguration church, under the floor, in a specially arranged crypt, lies the body of Archbishop Neophyte of Perm and Verkhoturye. In 1869, an iron grille with four cast-iron columns and a cast-iron plate with an inscription about the time and place of his death was installed over his grave. In 1877, a small icon case was arranged in the wall, where, according to Neophyte's will, his cell icons were placed. Under the left choir, the abbot of the monastery, Archimandrite Gabriel, was buried.

On January 19, 2015, a unique 16-ton bell was consecrated in the Spaso-Transfiguration Church of the Holy Nicholas Male Monastery in Verkhoturye. The idea of its casting belonged to the authorities of the Sverdlovsk region and was supported by Metropolitan Kirill of Yekaterinburg and Verkhoturye. A year later, the bell sounded for the first time on the territory of the monastery. The metropolitan noted that now the region has its own "Ural Tsar Bell," which will sound as the voice of Orthodoxy. The ceremony of consecration was attended by Governor Yevgeny Kuyvashev, who, together with the metropolitan, was the first to strike the bell. This bell weighs over 16 tons and is among the twenty largest in Russia. In calm weather, its sound can be heard from over 10 km away. The bell features six full-length icons: of the Holy Trinity, Saint Apostle Andrew the First-Called, Saint Nicholas the Wonderworker, the Royal Martyrs, Saint Martyr Tsar Nicholas II, and Saint Righteous Simeon of Verkhoturye.