The Church of the Intercession at the Trading Post was built on the site of an older church dedicated to Joachim and Anna. The construction of the Church of Joachim and Anna is linked to the visits of Tsar Ivan the Terrible to Vologda. His first visit to the city dates back to 1545. In 1549, a daughter named Anna was born to Ivan, and in honor of this event, a church dedicated to Joachim and Anna was laid in the Novodevichy Monastery. The wooden Church of Joachim and Anna in Vologda became the household church at the wooden palace of Ivan the Terrible in the 1560s. After the fire of 1605, the church was restored and was named Joachim and Anna at the Tsar's Sennaya, and in 1627, Joachim and Anna at the Old Tsar's Court. Architecturally, the church of the second half of the 17th century belonged to the type of cell churches.

After the fire of 1679, the church was restored with the main altar in honor of the Intercession of the Holy Virgin and a chapel of Joachim and Anna. The warm wooden church, likely rebuilt after the fire of 1698, stood until the 1780s. Elder Kirill Poyarkov and the parishioners received permission from Archbishop Irinei to build a stone church. It is known that during the construction, the wooden church was moved without interrupting services. After the stone church was completed, the old one was dismantled for firewood.

There are mentions of the Church of the Intercession in Vologda at the end of the 15th century, and chronicles state that it burned down in 1486. However, there is no precise data linking this church to the Church of the Intercession at the Trading Post. An indirect confirmation of the earlier origin of the Intercession church may be the existence of Intercession Street in the early 17th century, where the Tsar's court and the Church of Joachim and Anna were located.

The stone church with the main altar in honor of the Intercession of the Holy Virgin and chapels of Macarius of Unzha and Joachim and Anna was built between 1778 and 1780. Since 1832, the church became a summer, cold church, and became part of the Intercession-Kazan parish formed after the merger with the Kazan church on the Swamp.

In the mid-1920s, the church was closed and transferred to the regional archive, despite strict conditions imposed by the Soviet authorities for churches. The closure of the church, which housed two parish communities, the Intercession-Kazan and Nikolskaya Sennoploshchadskaya, caused strong protests from parishioners. Services resumed in 1992, and in 1995, a Sunday school opened at the church.