The history of the Intercession Church begins with a request from Irkutsk merchant Yermolai Lyachagov, submitted in September 1823 to Irkutsk Bishop Mikhail. Lyachagov asked for permission to convert his house into a church, adding an altar, porch, and bell tower in the name of the Intercession of the Blessed Virgin Mary and the chapel of Saint Martyr Yermolai at his own expense.

The church building project was developed by city architect V. Bronnikov. However, from March to September 1826, changes occurred, and in September of the same year, preparations were made for the consecration of the Sretensky and Pokrovsky chapels. On October 1, 1826, the church was consecrated in the name of the Meeting of the Lord and the chapel of the Intercession of the Blessed Virgin Mary by Archpriest Nikifor Parnyakov in the presence of Bishop Mikhail. However, the church remained without regular services, which puzzled the local residents. From March 26, 1827, the priest became Andrei Shastin.

By April 1828, the temple in the name of Saint Martyr Yermolai was completed and ready for consecration, which took place on May 7, 1828. The first clerical report of 1832 notes 43 households in the parish, where 244 men and 189 women lived. In 1838, the name of the elder Ivan Alexeev Lyachagov, a relative of E. Lyachagov, was mentioned for the first time.

From 1840 to 1843, the construction of a stone porch was carried out, completed by September 1843. Documents from 1844-1846 are missing, but in 1847, a two-story wooden house was purchased for the clergy. That same year, priest Vladimir Nikolsky died, possibly buried in the churchyard. On September 8, 1847, the church was reconsecrated.

The clerical report of 1857 mentions the wooden porch at the upper church for the first time. On January 8, 1859, a new bell, donated by Khrisanth Bryansky, was raised to the bell tower. In 1871, the church was surrounded by a wooden fence, and in 1875, a house for the priest was purchased thanks to a donation from merchant Pavel Andreevich Ponomaryov.

Pavel Andreevich Ponomaryov, suffering from deteriorating health, died in 1883. His remains were temporarily placed in a crypt in St. Petersburg and in 1890 were transported to his homeland and buried at the altar of the Intercession Church. In his honor, primary schools were opened in Irkutsk.

After 1917, following the devastation of the Znamensky Monastery, nuns were relocated to the Intercession Church. An auto base was established near the church, seeking to occupy its premises. The church needed repairs but was closed in April 1934 and used as workshops for an auto repair enterprise. Ponomaryov's tombstone was destroyed.

Since October 2007, the rector of the church has been priest Valery Nekrasov. The first service took place in 2008 on Easter. In 2011, Father Valery was awarded the title of archpriest. The church has three altars: the Meeting of the Lord, the Intercession of the Virgin Mary, and Saint Martyr Yermolai.