In 1902, the Mossy Creek community joined with other communities in the Jefferson City area. At that time, the Baptist Church of Mossy Creek changed its name to First Baptist Church of Jefferson City. Around the same time, students from Mossy Creek Missionary Baptist Church Seminary began conducting Bible studies on the north side of Mossy Creek. These gatherings eventually developed into a mission, and in September 1902, the Second Baptist Church of Jefferson City was formally constituted.

As the congregation grew, it was served by students from what is now known as Carson-Newman University. During the 1920s, the church changed its name to Northside Baptist Church. A larger building was constructed to replace the original facility and served the congregation for approximately forty years. A parsonage was also built during this period.

By the 1950s, the congregation had outgrown its existing facilities, creating a need for additional land. In 1969, the first building was completed at the church's new location. Because the church was no longer situated on the north side of town, the congregation chose a new name based not on geography, but on Scripture.

The church became Emmanuel Baptist Church, a name meaning "God with us." Located on Overlook Avenue, the congregation began construction of the present sanctuary in July 1976. Despite the many challenges encountered during construction and throughout the years that followed, the church continues to stand as a testimony to the presence, provision, and faithfulness of the Lord.

Today, Emmanuel Baptist Church remains grateful for the generations of believers who have faithfully served and worshiped here. The story of Emmanuel is ultimately a story of God's faithfulness—leading, sustaining, and building His church through more than a century of ministry.