In 1995, he became the manager of Stockport County, guiding the team to a League Cup semi-final and automatic promotion to the second tier of English football in 1997.

He left Stockport to become the manager of Southampton in the Premier League, where he stayed for over 100 games until he was suspended by the club in January 2000, after his arrest on charges of child abuse.

He was appointed manager of Sheffield Wednesday on 1 March 2012, guiding the club to finishing second in League One, thus gaining automatic promotion to the Championship.

He left Everton to play for Coventry City in 1979 for a transfer fee of £275,000 – after three seasons he picked up a knee injury which threatened to end his football career.

Jones first went to Hong Kong on 2 April 1981 on loan from Coventry City for the remainder of the season, teammate Jim Hagan had already settled in the squad.

After retiring from professional football he went on to become assistant manager to Bryan Griffiths at Southport, where he also made two appearances as a player, before they both left and took up identical roles at Mossley for the 1988–89 season.

In January 2000, Southampton decided to suspend him on full pay until the case was resolved, with Glenn Hoddle taking over his managerial duties.

He spent over £7 million – the largest spending in the club's history in one transfer period – bringing in the likes of Nathan Blake, Colin Cameron, Mark Kennedy, Alex Rae and Shaun Newton.

[5] Jones's new-look team quickly made an impact, hitting the top of the league by late September, and remaining in the automatic promotion spots over the following months.

By mid-March, they sat in second place, with an eleven point lead over their arch-rivals and nearest challengers West Bromwich Albion.

Jones suffered more disappointment when his side compounded their poor end to the campaign by losing their play-off semi-final to Norwich City.

Inconsistent early form left them well off the pace for automatic promotion and a dismal Christmas period saw him under increasing pressure as they weren't even in the playoff zone.

An FA Cup win over top flight Newcastle United seemed to reverse fortunes though, and his side lost just two of their remaining twenty games to finish fifth, in the play-off zone.

They overcame Reading in the semi-finals and 3–0 victory over Sheffield United in the final at Millennium Stadium, Cardiff, saw Jones become the manager who returned Wolves to the top level of English football for the first time since 1984, and the man who achieved the chairman Jack Hayward's ambition of Premier League football after eleven years, millions of pounds spent on players and four previous managers.

However, the team was significantly weakened by long-term injuries to Joleon Lescott and Matt Murray, and began the season missing several other key components of their promotion campaign.

The side endured a very poor start to the campaign, shipping nine goals in two games, and remaining winless until their eighth match.

He faced an FAW hearing about the incident and was found guilty, resulting in a two-match touchline ban, which he served in the Championship match against Plymouth Argyle and the third round FA Cup tie against Chasetown.

[8][9] On 9 March 2008, Jones led Cardiff to their first FA Cup semi-final tie since 1927 after beating Premier League side Middlesbrough 2–0 in the quarter-finals.

The start of the 2008–09 season saw veterans Jimmy Floyd Hasselbaink, Robbie Fowler and Trevor Sinclair released and the sales of some of the team's biggest assets in Glenn Loovens and Aaron Ramsey.

On 7 November 2009, Jones earned the Championship Manager of the Month for October, the same day Cardiff lost the first South Wales derby 3–2 at Liberty Stadium.

At the end of the season, Jones took Cardiff to their highest finish in the league in 39 years, fourth place, meaning they would take part in the play-offs.

Cardiff beat Leicester at the Walkers Stadium 1–0, thanks to Peter Whittingham's free kick but lost the second leg 3–2, resulting in extra time.

[21] Notified of this public criticism afterwards, Jones told reporters that Stelling showed a "lack of respect" and accused him of being "hypocritical", having been in his office when Hartlepool had gone five games without a loss.

[23] Despite Hartlepool winning their final game of the season against Doncaster Rovers, a late goal from Newport consigned Pools to relegation from the Football League for the first time after joining in 1921.

In June 1999, Jones was formally questioned by police over alleged sexual abuse at St George's School in Formby, Merseyside, a home for children with educational and behavioural problems, where he had been employed as a care worker from 1986 to 1990.

[28] After a further alleged victim declined to appear or refused to give evidence, the judge directed the jury during the fourth day of proceedings to return a formal not guilty verdict on four charges relating to the absent party.