During the election of the Kansas's first territorial legislature, on March 30, 1855, Jones led a group of pro-slavery men that destroyed the ballot box at Bloomington, Kansas. This action coupled with his pro-slavery sentiment prompted his appointment on August 27, 1855, as first sheriff of Douglas County by the acting Governor Daniel Woodson. Jones executed his new responsibilities with much zeal, suppressing the rights of the free-state men under his jurisdiction and fostering an atmosphere of distrust.
Violence marked the tenure of Sheriff Jones in Douglas County, beginning in November 1855. A free-state man by the name of Charles W. Dow was murdered ten miles south of Lawrence by Franklin N. Coleman, a proslavery man. Immediately after the murder, a friend of Dow's, Jacob Branson, was arrested for attending a free-state protest meeting. He was quickly freed by free-state partisans, but the arrest so alarmed the free-state community that it began to organize a militia and fortify the town of Lawrence. The "Wakarusa War" ensued whereby proslavery militia supporting Sheriff Jones and the governor besieged the city for about a week. On December 8 and 9, James H. Lane and Charles Robinson brokered a truce with Governor Wilson Shannon. Thereafter both sides disbanded, and the war came to an official end.
Soon, however, renewed violence erupted between free-state and proslavery settlers in Douglas County. George W. Brown's free-state newspaper in Lawrence, the Herald of Freedom, had long been a source of bitter contempt to the proslavery forces operating in Kansas. On May 21, 1856, Sheriff Jones, accompanied by a group of proslavery men acting as his posse, entered Lawrence intent on destroying the offices of the Herald of Freedom and the Kansas Free State . In the raid that followed they destroyed the newspaper offices (dumping their type in the Kansas River), looted several other businesses, and burned the Free State Hotel (later the Eldridge House). This action became widely known as the "Sack of Lawrence."
On January 7, 1857, the tenure of Jones as sheriff of Douglas County came to an end, and he left Kansas Territory. Jones resigned as sheriff of Douglas County in a heated dispute with the territorial governor. The source of the disagreement was the governor's denial of the sheriff's request for "balls and chains" for use on incarcerated free-state men at Lecompton. Jones clearly wanted to impose harsh corporal punishment on his adversaries, and failing to win gubernatorial support for such measures, Jones chose resignation over a more lenient, conciliatory policy. Jones quickly left the territory, moving to New Mexico, where in September 1858 he accepted an appointment as collector of customs at Paso del Norte and eventually purchased a ranch near Mesilla, where he died some years later.