Later career
Gregory's next spell in management was with Derby County (January 2002 – March 2003). When he took charge at Derby they were bottom of the Premiership, but after winning both of his first two games at the helm it looked as though he might be able to save them from relegation. Unfortunately, seven defeats from their final eight fixtures saw Derby slip out of the Premiership after six years. The club's financial problems meant that Gregory hadn't purchased any players during the 2002–03 season, and their subsequent form in Division One was disappointing.
He was dismissed in March 2003 for alleged misconduct but later won £1 million in compensation for unfair dismissal. Due to the ongoing lawsuit, Gregory was unable to apply for another managerial position for some time, so he spent most of the next three years working as a television pundit.
On 20 September 2006, he was unveiled as manager of Queens Park Rangers. He replaced Gary Waddock, who had stepped down following a poor succession of results that had left the club bottom of the Football League Championship. This appointment caused a schism among QPR fans, some of whom saw Gregory's friendship with controversial chairman Gianni Paladini as a conflict of interest. After a decent start with successive victories over Hull City and Southampton, Rangers form dipped before winning three consecutive matches (including a victory at (then) league leaders Cardiff City). However, results did not continue to improve, and relegation looked a distinct possibility for Gregory's team. But following a fine late season run, QPR defeated Cardiff 1–0 at Loftus Road on 21 April 2007 to secure their Championship status for another year. Gregory was dismissed as QPR manager on 1 October 2007, after some poor performances.
On 8 December 2009, Gregory was appointed the manager of Israeli club Maccabi Ahi Nazareth.
On 18 May 2010, Gregory signed a three-year contract with Israeli Premier League Club Ashdod. He resigned from Ashdod on 18 April 2011, with the club facing the possibility of relegation.
On 13 June 2011, Gregory was appointed the manager of Kazakh club Kairat from Almaty, Kazakhstan. Kairat survived relegation at the end of the 2011 season to the second tier of Kazakhstan football.
Gregory had his contract as manager of Kairat terminated in December 2011, and in April 2012 was paid $120,000 in compensation.
On 3 December 2013, Gregory was named as the manager of Crawley Town, replacing previous manager Richie Barker.
On 27 December 2014, after being Crawley Town manager for just over a year Gregory stepped down as manager due to health problems; on the same day Crawley Town named Welsh former international and former Wolverhampton Wanderers manager Dean Saunders as interim manager.
On 3 July 2017, Gregory signed as head coach of Chennaiyin in the Indian Super League.
On 17 March 2018, he led Chennaiyin to their second Indian Super League title by defeating Bengaluru 3–2 in the finals. On 19 March 2018, Gregory extended his contract for one year; he later resigned after a poor run of form in the 2019-20 season.
