Jones began his career with Football Conference club Merthyr Tydfil before joining Luton Town in the summer of 1995.

In November 2022, he left Luton for a second time and joined Premier League club Southampton, but lasted just three months in the role before he was sacked.

Jones was born in Blaenrhondda, a small mining village in the Rhondda Valley, and began his career with the youth team at local club Cardiff City.

[3] Jones was released by Cardiff in the summer of 1991 and went to play for Maesteg Park, Ton Pentre and Football Conference club Merthyr Tydfil.

[5] However he soon became homesick at Luton and so moved to Spain to join Segunda División club Badajoz who were managed by Englishman Colin Addison.

[9] His seven-year association with the club included captaining the team at Wembley Stadium for the 2007 Football League One play-off final, resulting in a 2–0 defeat to Blackpool.

[15] On 1 June 2012, Jones left Yeovil Town by mutual consent after seven years and having played 211 matches for the club.

[21] On 3 February 2015, after the appointment of Colin Calderwood as Hughton's assistant manager, Jones was demoted to the role of first-team coach.

[22] On 6 January 2016, Jones left his role as first-team coach with Brighton to become the new manager of League Two club Luton Town on a two-and-a-half-year contract.

[25][26][27][28] Jones' Luton team spent only one week of the season outside the top seven positions,[29] while he also led the club to the semi-final of the EFL Trophy.

[35][36] Jones was named the League Two Manager of the Month for October 2017 after Luton recorded three wins, one draw and one defeat,[37] including a 7–1 home victory over Stevenage.

[39] Luton's win over Cambridge meant they became the first team in the history of the English Football League to score seven or more goals on three occasions before Christmas.

[40] They were also the highest-scoring team in the country in early December with 63 goals in all competitions, one more than Manchester City who were top of the Premier League.

[47] Jones continued to take Luton on an upward trajectory during the 2018–19 season, leading the club to second place in League One by January 2019 with the highest number of goals scored.

Following the dismissal of Gary Rowett, he was linked to the vacant managerial job at Championship club Stoke City in January 2019.

[48] His departure was announced later the same day and he left Luton with the highest Football League points per game ratio of any manager in their history.

[66] On 20 December 2022, Jones secured his first competitive victory in Southampton's 2–1 win against Lincoln City in the EFL Cup.

[77] Nathan Jones does not hide his faith and is very open to mentioning it during press conferences, occasionally appending 'God willing' to his hope that his tactics work.