In 1944, a small group began meeting in a tiny cabin on Sunday afternoons. Two years later on July 7, 1946, under the leadership of Pastor Richard Halter, a nucleus of ten people organized into an independent Baptist church. The original name was the Fundamental Baptist Church. The Lord blessed the work and the small church began to grow. Soon they were able to purchase property and construct a building. Due to the structure's location on Main Street in Harbor Springs, a decision was made on July 6, 1949 by congregational vote to change the name to the Main Street Baptist Church. Reverend Halter continued to pastor Main Street Baptist until 1964.

At this point, the church called Rev. James Cranick who pastored here until 1969. In 1970, Rev. James Sweet took the pulpit. Pastor Sweet served this church and this community for twenty years and the church was blessed under his leadership. Near the beginning of his ministry, Main Street Baptist Church bought the present parsonage at 535 E. Lake Street and tore down the deteriorating former parsonage which sat next to the church building to make room for what is still the church parking lot.

In 1990, Pastor Sweet resigned and Rev. Donald Phillips accepted the calling to pastor MSBC. Then in January, 1993, Rev. Jim Wright took the pulpit. He pastored until 1999. Pastor Mike Smith accepted the pastorate and ministered here until 2003. Pastor Dennis Rew served as our pastor from June, 2004, to February, 2017. Pastor Terry Morse grew up in Harbor Springs, was a missionary to France, French Polynesia, and Canada. He began to minister here in March 2017 and pastored until January 2023 where Pastor Gary Costanza is now currently serving as the pastor.

A look at our history convinces us of God's sustaining power, without which this little church would have passed out of existence long ago. That we are still faithfully standing firmly on the foundation of Scripture assures us that God's purpose and plan for this ministry has not been retracted. The continuing ministry of this assembly is to be a spiritual lighthouse to Harbor Springs and the surrounding areas. It is our prayer that, by His Grace and in accordance to His Will, the light of this church will shine ever brighter as the days get darker, until Jesus returns to take us home to Glory.