After a brief spell at Derby County together the two men went their separate ways, and after Jones had two years in charge of Halifax Town he then joined Peterborough, initially as Noel Cantwell's assistant, before taking over as manager in 1988.
It was at Peterborough that Jones met Neil Warnock who he would go on to assist at Notts County from 1989 to 1993, and Huddersfield Town from 1993 to 1995, before joining Plymouth Argyle in 1995, once again as Warnock's assistant. After Warnock left Argyle in 1997 Jones had a short, unsuccessful spell as manager at Home Park and on being dismissed in 1998 had a spell managing the Brunei national team, performing an amazing feat in getting the tiny Borneo province to their first ever Malaysia Cup final in 1999, beating Sarawak by two goals to one to collect the trophy.
Jones remained with Brunei until 2002, returning to England for spells as assistant manager at Nuneaton Borough, and then manager of Telford United before financial problems led to the collapse of the club.
In 2005, Jones resumed his partnership with Warnock at Sheffield United. The club were promoted to the Premiership at the end of Jones' first season at the Blades, but were relegated again twelve months later, with both Warnock and Jones stepping down.
After this the two men spent a short period out of football before joining Crystal Palace in October 2007, with the Eagles turning from relegation battlers to play-off semi-finalists under Warnock and Jones' stewardship.
On 1 March 2010. Jones joined Neil Warnock at London rivals Queens Park Rangers, as assistant manager. However on 8 January 2012, Warnock was sacked as manager of QPR. Jones and Keith Curle were also reported to have left the club.
On 19 February 2012, new Leeds United manager, Neil Warnock confirmed Jones would be his assistant manager. On 1 April 2013 When Warnock was sacked as manager of Leeds UnitedJones left the club.
On 21 June 2013 Jones was appointed assistant manager at Notts County. He left the club following Chris Kiwomya's departure.