He was made captain of the Under-19s at the start of the 2002–03 season, and went on to make 18 appearances, scoring one goal, as the team progressed to the final of the FA Youth Cup in April 2003, where a 2–0 victory over Middlesbrough in the second leg saw him lift the trophy at Old Trafford.

He was named as a substitute for a League Cup tie against West Bromwich Albion in December 2003, but did not feature in the game.

Jones was allocated a squad number, 31, during the 2003–04 season and made his senior debut as a late substitute in a 1–0 home win over Arsenal in the League Cup.

He made his full team debut in Manchester United's shock 0–0 home draw with non-league Exeter City in the FA Cup third round.

Despite these opportunities Jones found it hard to break into the first team ahead of Roy Keane and Paul Scholes and spent much of the remainder of his Manchester United career either in the reserves or out on loan.

Good performances from the bench soon saw him established as first-choice in midfield and he scored his first goal for the club in a 4–0 away win at Ipswich Town on 29 August 2005.

Jones played a key role in a long unbeaten run which pushed Preston up into the Championship play-off positions, making 24 appearances, including three as substitute, and scoring 3 goals.

Jones' spell at Preston was followed by joining Eredivisie side NEC Nijmegen on a loan deal until the end 2005–06 season.

Wearing number five, he again had to spend time on the substitutes bench to begin with, but impressed sufficiently in brief appearances against Ajax and Sparta Rotterdam to be brought on at half-time against ADO Den Haag on 22 January 2006.

Despite his success in the Netherlands, the arrival of £14 million Michael Carrick from Tottenham meant Jones was restricted to appearances in the League Cup.

[5] Despite Derby struggling on their return to the top flight Jones was unable to force himself into the first team on a regular basis, playing only 15 times in the league.

[6] He made his Wolves debut on the opening day of the 2008–09 season at Plymouth Argyle and scored his first goal in a 5–1 win over Nottingham Forest on 30 August.

Jones' return to the top flight was initially curtailed by several injury setbacks to a troublesome knee problem that had occurred in the previous season.

[7] However, he returned to the central midfield in early 2010 at the expense of Nenad Milijaš and scored his first Premier League goal for Wolves when he finished an 18-pass move to defeat Tottenham Hotspur.

[11] Jones scored the fifth goal in the game in a 5–0 win over Doncaster Rovers putting Wolves through to the next round of the FA Cup.

[28] On 1 June 2022, after his contract as a player-coach ended, Wrexham offered Jones the opportunity to continue in his role as the Club's First Team Coach.