During the Obama administration, he voted against the Republican Path to Prosperity budget proposal of 2011, after which he was removed from key committee roles for defying party leadership.

In the run-off election, he was defeated by Eva Clayton, Chairwoman of the Warren County Board of Commissioners, by a margin of 55–45%.

[10] In 1994, he switched parties and ran in North Carolina's 3rd congressional district, which had absorbed a large chunk of his father's former territory.

[12] With his victory, Jones became the first Republican to represent a significant portion of Eastern North Carolina in the House since Reconstruction.

Jones garnered 61% of the vote in that contest, largely helped by George W. Bush, winning the 3rd with his highest victory margin in the state.

[15] Jones' change of heart on the Iraq War (see below) resulted in him facing serious primary opposition for the first time since his initial run for Congress.

[20] He faced Taylor Griffin, a former aide to President George W. Bush, who was heavily supported by outside money, and won the Republican Party primary on May 6.

"[4] Jones drifted towards the libertarian spectrum when he changed his positions on foreign policy including the Iraq War.

Jones opposed pork barrel spending projects[4] and was a staunch advocate of federal prohibition of online poker.

[33] In an annual survey conducted by Washingtonian magazine, congressional staffers voted Jones the kindest member of the House.

[4] In 2007, Jones cosponsored legislation with fellow North Carolina congressman Heath Shuler to require airlines to have sections of the aircraft where large movie screens were not visible.

[34] He also was the only Republican co-sponsor of legislation to challenge Tom DeLay's proposed changes to House ethics rules.

[4] On February 14, 2008, Jones was one of only three Republicans (along with Ron Paul and Wayne Gilchrest) to vote to hold George W. Bush confidantes Joshua Bolten and Harriet Miers in contempt of Congress for failing to testify and provide documents relevant to the firing of federal prosecutors.

Jones was removed from the Financial Services Committee, a plum seat for fundraising, ostensibly as reprisal for not raising money for the Republican Party.

[45] On March 28, 2017, Jones became the first Republican Congressman to call for Representative Devin Nunes to recuse himself as chairman of the House Intelligence Committee, and for the establishment of an independent commission to investigate Russian interference in the 2016 presidential election.

[46] He cited the alleged impropriety of Congressman Nunes' meeting at the White House the previous week as the reason for breaking with his party on the issue.

[51] On March 17, 2005, he sponsored a bill endorsing the conduct of his Camp Lejeune constituent, controversial Marine Corps Lieutenant Ilario Pantano, who faced charges (subsequently dropped) for having shot two Iraqis (allegedly unarmed civilians) on April 15, 2004.

On June 16, 2005, he joined with three other members of Congress (Neil Abercrombie, Dennis Kucinich and Ron Paul) in introducing a resolution calling for the start of a withdrawal of U.S. forces from Iraq to begin by October 2006.

[4] He said, "If we were given misinformation intentionally by people in this administration, to commit the authority to send boys, and in some instances girls, to go into Iraq, that is wrong.

"[4] In 2007, he and Rep. William Delahunt (D–MA) introduced the Constitutional War Powers Resolution, which sought to "prohibit the president from ordering military action without congressional approval, except when the United States or U.S. troops were attacked or when U.S. citizens needed to be evacuated.

[56] According to Jones on his web site, the resolution requires that – absent a national emergency created by an attack, or a demonstrably imminent attack, by Iran upon the United States or its armed forces – the President must consult with Congress and receive specific authorization prior to initiating any use of military force against Iran.

[57] This resolution was removed from a military spending bill for the war in Iraq by House Speaker Nancy Pelosi (D–CA) on March 13, 2007.

[58] On March 23, 2007, Jones was one of two Republicans to vote for a bill that would have required President George W. Bush to bring combat troops home from Iraq by September 1, 2008.

He was passed over for Randy Forbes when the 110th Congress convened because the full committee's ranking member, Duncan Hunter of California, did not agree with Jones' change of heart on the war.

[61] Additionally, Jones' changed views on the war and other issues angered many Republicans in his district, which has the largest military presence of any in North Carolina.

"[63] In the wake of the 2016 Orlando nightclub shooting, Jones put out a press release calling it "horrific and senseless."

[73][74] In July 2018, Jones began to miss votes due to illness; in December of that year, the House granted him a leave of absence for the remainder of the session by unanimous consent.