Land near the present church site was provided to New Bethel Missionary Baptist Church by Mrs. Florida Thompson of a prominent white Germantown family for a brush arbor where enslaved people could worship and learn to read and write. After emancipation, the land was purchased from Mrs. Ellza Corneltus for $200 in 1869. In 1886, under the leadership of its first pastor, Rev. Isaac Cotton, Germantown School opened on part of the land, and philanthropist Julius Rosenwald of Chicago provided construction funds. The school was renamed Neshoba School in 1912 and by 1917 was known as Neshoba Junior High School, remaining in operation until 1969, when desegregation and school consolidation led to its closure. During its years of operation, dedicated principals and educators stressed education and knowledge for all students, many of whom went on to become productive citizens despite living through segregation, while New Bethel Missionary Baptist Church continued as a place of worship into the 21st century under Pastor Dr. Donald R. Ester.