His parents Henry and Nancy (Robertson) Jones were of Welsh descent and moved to the area that became Travis County, Texas when John was four years old.
After the war, he moved briefly to Mexico with the purpose of locating and founding an exile colony for former Confederate supporters, but he returned to Texas after the attempt failed.
In 1874, and after a short incursion in politics, he accepted the offer of commanding a newly formed branch of the Texas Rangers, named the "Frontier Battalion."
In the following years, Jones engaged in battle with the Comanche, the Kiowa and the Apache on several occasions, and the Frontier Battalion under his command was instrumental in ending the Indian incursions and raids over the settlers' homesteads.
His force also played a major role in pursuing and capturing many criminals and outlaws, such as noted bank robber Sam Bass in 1878.