Sandy Run Missionary Baptist Church was established in 1854 under a large tree across the street in front of the church's current location. Under the leadership of the church's first pastor, Rev. Coleious Scott, members worshipped for a long time under a bush shelter during the days of slavery. ​

In 1864, a log church was built in the same spot; subsequently moving across the street and building a framed facility where the church now stands. Other ministers contributing to the forward march pf the were Rev. George Rhodes, Rev. B.E. Davis, Rev. M.D. Standford, and Rev. J.E. Kornegay. ​

In 1942 Rev. E. W. Wooten became the new pastor and led a plan to erect the church's first brick building; the new building was erected in 1953 at an estimated cost of $68,000. The church grew from having one Sunday per month service to a full-time church with modern facilities and a parsonage. ​

On December 16, 1970 after having launched a drive to build a housing project for the Jacksonville community Rev. Wooten and church officers closed on a $2.5 million federal housing project for low income families. During that same month construction began on 151 units, a day care center, and a washerette.​

Other ministers who made their contribution to the forward march of Sandy Run Missionary Baptist Church were Rev.  A. G. Mullen, Rev. Cleophis Wright, and Rev. Johnny Pearson. 

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