Following a poor start to the 2017–18 season, with the club in the relegation zone heading into the new year, he was dismissed by Stoke on 6 January 2018, hours after an FA Cup third round exit to League Two side Coventry City.

The departure of Wilkins to Milan at the end of the season saw manager Ron Atkinson decide to stick to using Whiteside in the centre of midfield, enabling Hughes to keep his place in the first team ahead of new signing Alan Brazil, and he was rewarded handsomely as he scored 25 goals in 55 matches across all competitions as United achieved an FA Cup final victory over Everton.

On 11 November 1987, he played two competitive matches in one day, first for Wales against Czechoslovakia in Prague in a Euro 1988 qualifier, and second, after being flown across the border into West Germany, appearing as a substitute for Bayern in their second round cup replay over Borussia Mönchengladbach.

They had gone ten league matches without a win in the autumn but then went on a strong run after the turn of the new year to lift them to third place, only for a late season collapse to drag them down to mid-table.

Eric Cantona was eventually signed at the end of November, which prompted interest from Newcastle United manager Kevin Keegan, who had first asked Ferguson about Hughes's availability that summer.

Perhaps the most memorable of those goals came in April 1994, when he scored a spectacular equaliser in the final minute of extra time in the FA Cup semi-final against Oldham Athletic at Wembley.

[16][17] Hughes left Old Trafford for the second and final time in June 1995 when he was sold to Chelsea for £1 million, in a summer that also saw the departures of players such as Paul Ince (to Inter Milan) and Andrei Kanchelskis (to Everton).

In their Euro 2004 qualifying group, Wales ended up second, beating Italy 2–1 in Cardiff in the process, but was denied a place in the final tournament after losing to Russia in the playoffs.

[35] In his second season, he helped Blackburn finish inside the top six of the Premier League and subsequently qualify for the UEFA Cup, beating teams such as Chelsea, Manchester United (twice) and Arsenal en route.

[48] The following day, Blackburn agreed to a then-world record compensation package for Hughes to take over as manager of Manchester City, and he was appointed as head coach on 4 June 2008 on a three-year contract.

[49] Following the appointment, Manchester City's executive chairman Garry Cook stated, "The Club intends to invest in new players as well as securing the long term services of key members of the current first team squad.

[53] Hughes was very active in the January 2009 transfer window, signing Wayne Bridge from Chelsea, Craig Bellamy from West Ham and Shay Given from Newcastle, as well as Nigel de Jong from Hamburger SV.

[54] In the summer of 2009, Hughes added Gareth Barry from Aston Villa, Roque Santa Cruz from Blackburn, and Emmanuel Adebayor and Kolo Touré from Arsenal to his squad, while Carlos Tevez also joined after his two-year deal with Manchester United expired.

In addition, Hughes signed defenders Joleon Lescott from Everton for a reported £22 million, and Sylvinho – a former Arsenal and double Champions League winner with Barcelona – on a free transfer.

[57] City then won 1–0 win over Wolverhampton Wanderers at Eastlands,[58] followed by Crystal Palace in the League Cup 2–0 and Portsmouth 1–0 to maintain a 100% clean sheet start to the season.

[67] On 10 January 2012, Hughes agreed terms with Queens Park Rangers and signed a two-and-a-half-year contract as their new manager, replacing the recently sacked Neil Warnock.

Despite scoring twice through Cissé and Jamie Mackie, two added time goals from Edin Džeko and Sergio Agüero earned City a dramatic victory and championship title.

[89][90] Hughes's first task was to release Rory Delap, Mamady Sidibe, Matthew Upson, Dean Whitehead, Carlo Nash and Matty Lund, at the same time giving Jermaine Pennant a new contract.

[97] On 2 September 2013, transfer deadline day, Hughes brought in Austrian forward Marko Arnautović from Werder Bremen and Stephen Ireland on loan from Aston Villa.

[109] For the 2014–15 season, Hughes signed Sunderland full-back Phil Bardsley, Fulham midfielder Steve Sidwell and Senegalese striker Mame Biram Diouf on free transfers.

[110][111] Also arriving for small fees were Slovakian defender Dionatan Teixeira and Barcelona forward Bojan, while wingers Victor Moses and Oussama Assaidi joined on season-long loans.

[140] Hughes also brought in Spanish striker Joselu for £5.75 million, Dutch midfielder Ibrahim Afellay, Shay Given, Jakob Haugaard, Glen Johnson and Marco van Ginkel.

[150] Stoke ended 2015 with a dramatic 4–3 win away at Everton, while they also reached the semi-final of the League Cup after defeating Luton Town, Fulham, Chelsea and Sheffield Wednesday en route.

[157] Stoke's form improved in February and March as they defeated Bournemouth, Aston Villa, Newcastle, Watford and earned a first Premier League draw at Chelsea.

[158] Following a season-ending injury to goalkeeper Jack Butland while on international duty, however, Stoke lost their defensive organisation:[159] They let a 2–0 lead slip against Swansea to draw 2–2 and then went and conceded four goals in three successive matches, against Liverpool, Tottenham and Manchester City.

[161] Hughes spent £18 million in July 2016 to bring in Welsh midfielder Joe Allen and Egyptian winger Ramadan Sobhi,[162][163] while defender Bruno Martins Indi and striker Wilfried Bony both joined on season-long loans on 31 August 2016 from Porto and Manchester City respectively.

[164] Departing the club were Joselu, Philipp Wollscheid and long-serving defender Marc Wilson, who left for Bournemouth after criticizing Hughes's defensive training on social media.

[165] Stoke began the 2016–17 season in poor form, drawing 1–1 away at Middlesbrough, then losing 4–1 to Manchester City, 1–0 to Everton and 4–0 to Tottenham, and 4–1 to Crystal Palace with chairman Peter Coates heavily criticising the team's performances.

[5] On 14 March 2018, Hughes succeeded Mauricio Pellegrino as manager of relegation-threatened Premier League club Southampton, signing a short-term contract for the remainder of the 2017–18 season.

[182] Despite a number of positive signings in the summer transfer window, Southampton made a poor start to the 2018–19 season and on 2 December 2018, with the club 18th in the table, Hughes was dismissed.