The St. John's congregation dates its origins to the 1742 arrival of Dr. Henry Melchior Muhlenberg, the father of the Lutheran Church in America. He stopped for two days in Charleston on his way to visit the Salzburger colony at Ebenezer, Georgia. He returned a month later and spent three weeks waiting for a ship to Philadelphia during which time he held services, taught catechism to the children of the German residents, and held services with communion on Sundays. Two Georgia Salzberger preachers visited for a few days in 1753 and conducted services and gave the sacraments. Rev. John George Friederichs came in 1755 and organized the congregation. While it appears there were several educated and trained men conducting Lutheran services in South Carolina prior to this time, the organization of the congregation into a formal body and the hiring of a pastor seems to mark the beginning of Lutheranism in South Carolina (HSC).

Services were held in the French Huguenot Church until the first Lutheran church was completed in 1763. Frederichs left soon after laying the cornerstone of the new church in 1759 and was in turn replaced by Pastor Heinrich Burchard Gabriel Wartmann. Wartmann stayed for two years or less. It has been suggested that while Wartmann was a good speaker and diligent, he had a fiery disposition which seems to have alienated the congregation. Rev. John Nicolas Martin came in 1763. Martin dedicated the new building on June 24, St. John the Baptist Day, 1764. The congregation adopted the St. John's name at that time. Martin accepted a call to a new church in the interior in 1767.

The German Friendly Society was founded in 1766 by Michael Kalteisen and 15 other men, all members of the St. John's congregation, as a men's fraternal organization. It has always maintained close ties to St. John's. The society collected 34 pounds, 5 shillings, and 6 pence to purchase a clock for the church in 1775. The clock was later returned. The church observes a German Friendly Society Sunday, with members of the society walking en masse from their meeting hall on Chalmers Street each year in January.

The internal struggles within the church continued. Rev. John Severin Hahnbaum replaced Martin in 1767, but passed in 1770. The congregation was then taken over by his son-in-law whom he had trained. The new Rev. Daser was quite controversial in the church and the council, but not many parisioners, found him to be lacking and was soon discharged, though the church continued to financially support Hahnbaum's daughter and grandchildren (Muhlenberg). Henry Melchior Muhlenberg came down from Philadelphia in 1774 and was able to unite the factions within the congregation to petition London for a new pastor. Pastor Martin returned from the upcountry to lead the congregation that year, but was expelled by the British two years later in 1776 for his refusal to lead prayers for the king during church services.

Rev. Christian Streit, the nation's first military chaplain, served as pastor until he was arrested in 1780 for his frequent criticism of the British. Streit is credited with introducing the first English sermons to the church. He did not return after his arrest and served the remainder of his career at a church in Winchester, Virginia. He was replaced at St. John's by the returning Rev. Daser who remained for five years this time before also removing to Virginia where he too ended his preaching career. Martin was recalled for a second time in 1786. He served as pastor for a year before retiring in 1787. He died in 1797 and is buried in the church burying ground.

Jacob Sass played an important role in shaping the church during this period as congregational president from 1807 to 1836. His twenty-nine year tenure included the hiring of the church's single most prominent pastor, construction of a new sanctuary, parish building, and numerous other improvements. The loss of church records for this period make it difficult to determine his exact role, but considering the accomplishments made during this period they must have been considerable.