The congregation took down much of the original log cabin and built a church on the site. Construction cost over $3,000. The church became known as the pepperbox church because of the square shape of the belfry. The church was used up until 1863, when the Union Army began their occupation of Chattanooga. The Army used the site as a makeshift hospital and part time prison.
After the war, the building was in terrible condition. It is thought that the army tore up much of the building to provide themselves firewood. After the Union occupation, the building was put up for sale. It was purchased by the the First Centenary United Methodist Church, the first independent, African American congregation in Tennessee after the Civil War. Soon after First Centenary began repairs on the building, it was destroyed by arson. In 1887 they rebuilt the church that now stands on the site.
In 1978, the building was declared unsafe. The congregation raised money to restore the roof and reveal much of the interior woodwork.