The Church of the Holy Trinity was built on the site of two old wooden churches, the Trinity and the Epiphany, thanks to the funding from the streltsy and haiduk regiments that defended the Novodvinsk fortress. Initially, these churches were located in the fortress on the Brovennik Island at the mouth of the Northern Dvina. In 1716, after the regiments were moved to the shore of Kuznechikha, the wooden churches were dismantled and relocated.

The new church was two-storied: on the upper floor was the Trinity church with a chapel of John the Baptist, and on the lower floor, the Epiphany church with a chapel of Archangel Michael. In 1761, a bell tower was added to the church.

In 1810, the church was transferred from battalion management to the diocesan authority, although most of the parishioners remained military personnel. Four regimental banners from the era of Peter I were kept here, and military ceremonies of the Arkhangelsk garrison were held.

During the Soviet era, the church was looted, the dome and bell tower were partially destroyed, and the building was successively used as a driving school, a workers' dormitory, and soap and stone-cutting factories. The last rector, Archpriest Nikolai Danilovich Rodimov, was executed in 1938 and canonized in 2006 as a new martyr and confessor of Russia.

In 1992, the church was returned to the Arkhangelsk diocese, and in 1995, the first service was held there. A social and charitable service is actively working at the church, and the restoration of the building continues.