According to legend, the name "middle mountain" descended from some clerk Munehisa Misuri, who lived in the first half of the 16th century and who was renowned for his charity work in relation to God's churches. Respected local historian Okulich-Kazarin N. W. chose the most plausible version of the origin of the name of the Church from small bogs, bearing the name of Mary, because these marshes once in ancient times and was surrounded by a mountain.

The construction of a stone Church occurred in 1547. Originally the Church was monastic. In the records of the scribe book 1623 mentions male'nikovo monastery please contact with the mountains. It is about this monastery is written in the Lives of mineah Russian Metropolitan Macarius. There is an assumption that the Abbot Kotelnikova monastery during the 60 years of the 16th century was Basil-Barlaam, who is the author of lives of Alexander Nevsky, the euphrosynus of Pskov.

In 1808 the Church was earmarked for demolition as a very old, but still the Holy Synod did not give consent to this action. In 1882, a merchant from Pskov Stepnowski Petr Mikhailovich front door was a stone built outbuilding. During 1892-1896, was carried out repair and restoration work on the funds of the Church warden – Kafelnikov Ivan Mikhailovich – honorary citizen of the city of Pskov. The Church has two altars, one of which is the throne of the Evangelist and Apostle John the theologian, and the second named in honor of the Holy Martyr John the Warrior. During 1786-1808, the Church was assigned to the temple with George of the Hill, and in 1934 he attributed the Church of Saints equal to the apostles Emperor Constantine and his mother Helena.

The Church tower was built at the same time with the construction of the Church of St. John the Baptist. The bell was hung with six bells. In the parish there were three chapels, built of wood: the Wonderworker and St. Nicholas, near the village of Krastanova, the Holy Martyr Anastasia and the Venerable Martyr Anastasia.

At the Church of St. John the Baptist existed hospice, parish guardianship, hospital, but a parochial school was never built. At the end of the 19th century in a village called Goat Brod was built a Church parish school, but soon in 1895 because of its proximity to other urban schools it was closed.

Around the perimeter of the whole Church cemetery where buried historian and researcher of Tzvelev S. A., restorer Smirnov V. P., as well as the soldiers who died during the execution of his military duty.

Since 1913, the temple priest Kolobov Fedor. In 1927, after he was arrested several times, Feodor Vasilyevich was exiled to the Urals. Wife Kolobov followed him, and after that any information not reported. The Sexton was a deacon Mikhail Lebedev, but of his later life nothing is known.

23 December 1936, it was decided to close the Church, but according to other sources, the services continued until the great Patriotic war. During the war the Church had received some damage to walls, roofing, interior and exterior finish. During 1970-1989, under the direction of architect Lebedev V. A. was a complete restoration of the Church. 3 March 1965 churchyard was closed for burials.

The first service began in 1992 at the very entrance to the temple. The revival of the Church of St. John the Baptist is closely intertwined with the name of the famous Abbot of Iona. Contributed to the restoration of the Church and Director of the Pskov cable plant Kukushkin Viktor Petrovich.
In 2001 Pskov Archbishop Eusebius performed the rite of consecration of eight bells, which were cast in the city of Voronezh, according to the ancient way. Today in the Church is a Sunday school and performed pilgrimage service, which received the status of a diocesan.