In 1779, a wooden church was built on the territory of the Intercession Cemetery by the order of the Governor-General of Livonia, J. J. Braun. Two years earlier, in 1777, there was a small wooden chapel located behind the Raghul gates on the site of an old military cemetery. The decree of the Pskov Spiritual Consistory No. 3985 dated November 6, 1779, ordered the construction of a church named in honor of the Intercession of the Holy Virgin. The chapel was transformed into a church, and the icons, altar, and iconostasis were taken from the field church of the Pskov Infantry Regiment, which had left its station near Riga. On December 4, 1779, services began in the church after the antimension was handed over by the Pskov Spiritual Consistory to the Riga Spiritual Administration.

In 1869, the St. Peter and Paul Brotherhood School was opened at the Intercession Church. In December 1875, a fire destroyed the wooden building of the Intercession Church. A competition was announced for the construction of a new church, and with donations from parishioners, a church was built according to the design of Robert Pflug. On September 9, 1879, the ceremony of consecration of the new stone Intercession Church was held, conducted by His Grace Philaret II.

Before the start of World War I, the interior of the church was dismantled and evacuated deep into the Russian Empire to avoid looting. The sacristy, bells, and iconostasis were removed. During the internal conflicts that engulfed the region, the church, which sought isolation, did not function and fell into disrepair. After the civil unrest and in the early years of the sovereign Latvian Republic, the church remained abandoned. Only in 1921, with the arrival of Ioann (Pommer) in Latvia, a champion of the Orthodox faith and Russian culture, did its restoration begin.