In the first half of the 18th century, the governor of Arkhangelsk, Ivan Petrovich Izmailov, approached Archbishop Varvara with a proposal: "Consider the possibility of burying the deceased outside the city..." As a result, a decree was adopted in Arkhangelsk prohibiting burials within the city limits to prevent epidemics and avoid "plague riots."

The Transfiguration Church at the first suburban cemetery did not last long. After it burned down in 1806 due to a lightning strike, a temple was built in honor of the Holy Prophets Elijah and Elisha in its place. The funds for the construction were provided by the well-known Arkhangelsk merchant of the first guild, Yakov Petrovich Nikonov, who left a significant mark in the history of the Pomor capital through numerous good deeds.

According to the chronicle, Nikonov, born into a spiritual family and working as an icon painter, helped his parents, and after their death, while still young and with limited means, took care of his brothers and sisters. He earned his initial capital through wholesale grain trading. Later, in Arkhangelsk, Nikonov purchased a house from advisor Alexander Zubkov, a brewery, and a sawmill in the Velikoustyug district. Due to his pious life, he became an honorary citizen of the city and served three times as the mayor of Arkhangelsk. In 1814, Yakov Petrovich represented the Arkhangelsk city community in St. Petersburg at the celebration of the Meeting of the Lord with Emperor Alexander I.

As a successful entrepreneur and philanthropist, Nikonov paid the salary of the city clerk from his own funds. He was buried in 1819 at the Ilyinsky cemetery at the entrance to the church he built himself.

By that time, the Transfiguration Church with a bell tower, which housed a charitable institution, was already standing next to it. The bell tower has survived to this day and is now used as a training bell tower for novice bell ringers.

In the 1920s, when the cathedral of the Holy Trinity in the city was occupied by schismatic renovators, the Transfiguration Church received the status of the main cathedral. However, in the 1930s, both parishes were closed, and the Transfiguration Church was dismantled for bricks.

During the Great Patriotic War, during a brief improvement in relations between the authorities and the church, the surviving Ilyinsky temple was returned to the Arkhangelsk diocese. In 1944, it was granted the status of a Cathedral, which it retains to this day.