The Church of St. Nicholas the Wonderworker in the village of Varzuga is part of the once extensive Petropavlovsky Varzuga parish, located on both banks of the river of the same name. Today, this is the territory of the Tersky District of the Murmansk Region, which stretches along the coast of the White Sea on the Kola Peninsula. In ancient times, the area was also called "Turiy," which referred to the entire peninsula. The first Slavic settlements here appeared as early as the 12th century, mainly consisting of migrants from Novgorod and Rostov-Suzdal lands. In the 14th-15th centuries, the area was already home to the estates of influential Novgorod boyars. In 1471, all these lands came under the rule of the Grand Prince of Moscow, Ivan III Vasilyevich. Since 1486, extensive lands in the Tersky region belonged to the Solovetsky Monastery, and later to the Antoniev-Siyensky and Spaso-Prilutsky Monasteries. Until 1682, the territory was part of the Novgorod Diocese, then of the Kholmogory and Vazhsky Dioceses.

In the 15th-16th centuries, the village of Varzuga was considered one of the largest on the "Turiy shore." According to the 1563 census, it occupied both sides of the river and had three wooden churches: St. Nicholas and the apostles Peter and Paul on the left bank, where most of the village was located, and the Assumption of the Blessed Virgin Mary on the right bank of the Varzuga River. The Assumption Church, the most well-known, existed earlier; the first mention of it dates back to 1491. This is confirmed by the tarhan letter of Archbishop Gennady of Novgorod, which exempted the Varzuga church, belonging to the Solovetsky Monastery, from archiepiscopal dues. It is believed that this letter refers to the Assumption Church, although there is an opinion that it concerns the Nicholas Church with the chapel of the Assumption of the Blessed Virgin Mary. In 1575, all these churches were mentioned as abandoned. The reason for the desolation was the punitive campaign of 1565, known as the "Basargin punishment." Only at the turn of the 16th-17th centuries were two more churches built in the parish. In 1597, "in the year 7105, on the 10th day of April," the Afanasievsky Church was erected, and shortly thereafter, the Zosimo-Savvatievsky Church. In the 19th century, there were two bell towers at the churches.

Of the five churches, four have survived to this day in varying degrees of preservation; the church in honor of Sts. Zosima and Savvatiy of Solovki was dismantled around 1877. They make up the Assumption and Nicholas church complexes. Of the two bell towers, only one remains, at the Assumption Church built in 1674. The other three churches have been rebuilt multiple times. The existing Church of St. Athanasius the Great, part of the Assumption complex, dates back to 1877, while the Petropavlovsky Church dates back to 1864.

The Church of St. Nicholas with the chapel of the Prophet Elijah is first mentioned in 1491 when it was "renewed" on the site of an older church of the Solovetsky Monastery. In the 16th century, the church was repeatedly mentioned in land books. It is likely that during this period there was a chapel in honor of the Assumption of the Blessed Virgin Mary. Information about its appearance and renovations until the end of the 17th century has not yet been found. Nevertheless, the existing church was rebuilt in 1705 with funds from local residents and was consecrated on June 28 and 29 according to the old style. The new church was a quadrangular log structure with a four-pitched roof, topped with five domes, one of which crowned the chapel. In 1851, a gallery was added to the western side of the log structure. In 1885, a new bell tower was built on the site of the dilapidated bell tower at the churches of St. Nicholas and the apostles Peter and Paul, but it has not survived to this day.

The bell set consisted of seven ancient bells from the 17th-18th centuries. In 1694, a resident of Kargopol donated a small bell: "In the year 202, this bell was bought for the Varzuga volost church of Peter and Paul and Nicholas the Wonderworker with church money by Kargopol's Ivan Andreev son Popov, weighing 25 poods 11 funt." Another bell weighing 13 poods was cast in 1755: "This bell was cast for the Church of Nicholas the Wonderworker in Varzuga, 1755. Cast by master Ivan Christoforov." The most interesting is the third bell weighing 125 poods, cast by masters from the famous family of foundry workers, the Lodygins: "This bell was cast by masters Yakov and Ivan Lodygins." The date of casting is unknown, but based on data about the activities of the masters from this family, it can be dated to the end of the 17th, beginning of the 18th century.

In the 20th century, the fate of the churches of the Varzuga parish was sad. Of the four churches, only one, the Assumption Church, has been restored. Both churches on the Nicholas side are in a deplorable state without domes, although services are held on festive days in the Petropavlovsky Church. The Church of St. Nicholas is still used as a store, with entrance through the altar.