The Baikalovo parish was founded in the early 17th century. The first church in the village was named the Nativity of Christ, although its history remains unknown, with mentions of it dating back to 1710. In the early 18th century, a wooden church in honor of the prophet Elijah was built, which burned down in one of the fires. In its place, the residents of Baikalovo rebuilt a wooden Elijah church. In 1779, a stone temple with two chapels was laid nearby: the main one in honor of the Intercession of the Mother of God, consecrated in 1800, and the northern one in honor of the Nativity of Christ, consecrated in 1797. In 1819, another chapel in honor of the Nativity of John the Baptist was consecrated in the bell tower. In 1860, the wooden church of the prophet Elijah was dismantled, but before that, in 1858, a new chapel of the temple in honor of the prophet Elijah was consecrated.

From 1879 to 1882, the temple underwent significant reconstruction: it was almost completely updated, expanded, and raised. The chapel in the bell tower was abolished, and the northern chapel was renamed in honor of the Nativity of John the Forerunner. The appearance of the temple changed significantly after the reconstruction, and the chapels were consecrated anew. The main chapel was consecrated in 1800. The height of the bell tower with the spire reached 51 meters, and the main bell, according to the memories of the old-timers, could be heard from 7 versts away in the village of Malkovoy. By this time, the temple was built not only from donations from parishioners but also from the income of shops and stalls that were used for the improvement of the temple. The priests received salaries from the state treasury.

By 1917, there were three priests serving in Baikalovo, assisted by a deacon and three psalmists. Traditions of holding fairs were established: a three-day one for the Feast of the Baptism, weekly ones for the Intercession and the Nativity of John the Forerunner.

The question of the church's fate became relevant in May 1925. Protocol No. 9 dated December 29, 1929, decided to close the church and transfer it to a club, marked "Not subject to public announcement." In the 1930s, the church lost its crosses, dome, and bell tower. The building housed a club for a long time, and later a Pioneer House.

On November 5, 1992, the parish was registered, and in 1993, the church building was returned to the believers. The temple is currently in the process of restoration.