During the Civil War, Johnathan Atkins served as lieutenant colonel of the Fifth Tennessee Regiment in the Confederate Army in 1861.

[6] The Tennessee Historical Commission describes him as key to defeating Reconstruction, saying he was "instrumental in obtaining removal of Federal troops from the South.

"[7] During the Forty-fifth and Forty-sixth Congresses, John was the chairman of the United States House Committee on Appropriations.

During his tenure as commissioner, Johnathan Atkins forbade the use of Native languages in reservation schools, stating in 1887 that "instruction of the Indians in the vernacular is not only of no use to them but it is detrimental to the cause of their education and civilization".

[9] A family friend who developed Atlanta's Atkins Park neighborhood named it in honor of the colonel.