Colchester United Colchester United decided to retain Dunne's services immediately after his retirement from the game by appointing him as a youth team coach, working under
Micky Cook. Dunne had previously done some scouting work for Colchester manager
Phil Parkinson towards the end of the 2002–03 season during his recuperation from his injuries. Dunne replaced Cook as senior youth team coach in August 2003. The young U's side then proceeded to the fifth round of the cup for the first time in the club's history after beating
Cardiff City 3–2 in the fourth round. Dunne's team booked their place in the quarter-finals of the competition with a 2–1 away win at
Crewe Alexandra in February 2005. A record youth fixture attendance at Layer Road saw 2,900 fans turn out for the quarter-final against rivals
Ipswich Town, but the weary Colchester players were thrashed 5–0 by Town on 16 March 2005. When Colchester United assistant manager
Mick Harford departed the club for a similar role with
Queens Park Rangers, Dunne was keen to once again stand in as assistant manager to
Geraint Williams having done so previously prior to Harford's arrival. In August 2007, following his good work with the Colchester United youth team, Dunne was promoted within the club to position of reserve team manager having managed the youth team for four seasons. With new assistant manager
Micky Adams leaving Colchester by mutual consent to concentrate on a return to full management, Dunne returned as stand-in assistant manager once again in January 2008 while remaining reserve team manager. With Geraint Williams dismissal as Colchester manager in September 2008, Dunne was once again drafted in as assistant manager while former-assistant manager
Kit Symons took up caretaker duties until a new manager was found.
Paul Lambert replaced Williams as Colchester manager. In the summer of 2009, Lambert brought in
Gary Holt as
player-coach, assisting the youth team and Joe Dunne, meaning Dunne could step up to first-team coach duties. but a little under one year later, Lambert walked out on the U's for
League One rivals
Norwich City. Dunne stepped in to take temporary charge of the first team as caretaker manager. Dunne's first game in charge was against his former club Gillingham on 18 August 2009, as the club put the loss of Lambert behind them to claim a 2–1 victory and remain top of League One.
MK Dons ended Colchester's 100% start to the
2009–10 season with a 2–1 victory on 22 August. Dunne ruled himself out of the running for the managers position at the club, stating that he was not one of the 12 possible candidates being interviewed for the job. Dunne suffered his second successive defeat as U's boss when
Leeds United visited the
Colchester Community Stadium on 29 August,
Aidy Boothroyd was announced as Lambert's successor, as Dunne took charge of Colchester for his final game as caretaker manager. The U's once again faced Gillingham, this time in the Football League Trophy as they bowed out on penalties after the game finished 1–1 in normal time. Dunne said of the experience as caretaker that he "enjoyed the pressure and he enjoyed the challenge" and that "it made him better and made him want to get better", whetting his appetite for more. , whom Dunne succeeded as
Colchester United manager Boothroyd left the U's in May 2010 for
Coventry City, as Colchester chairman
Robbie Cowling announced that both Boothroyd's former assistant
John Ward and Dunne were both in the running for the managerial position. On 31 May, Ward was confirmed as the club's new manager, and Dunne was promoted once again to the position of assistant manager. Following Ward's dismissal as Colchester manager on 24 September 2012, Dunne was once again made caretaker manager as Cowling began his search for a new manager. However, three days later on 27 September 2012, without managing a game as caretaker, Dunne was appointed full-time manager of Colchester United on a one-year rolling contract. He named former Colchester United midfielder and friend Mark Kinsella as his assistant. Dunne immediately signed three players on loan; forward
Jabo Ibehre from MK Dons and
Arsenal duo
Craig Eastmond and
Sanchez Watt, All three players went straight into the first team squad for Dunne's first match as Colchester manager against
Hartlepool United. After falling behind in the sixth minute, Colchester hit back with goals from
Gavin Massey and two from new signing Ibehre to win 3–1. After winning four of his first seven games, ending the club's eight-game winless start to the
2012–13 season, Dunne considered quitting the club in January 2013 following a record ninth consecutive loss for Colchester, with the club struggling at the lower end of League One. However, he stayed on to help the U's narrowly avoid relegation to
League Two with a final-day 2–0 win at Carlisle United, the club finished 20th in the league table. With Cowling's and Dunne's emphasis on producing quality players raised through the Colchester United
Academy and blooding them for first team action, Dunne said he was "fine" with the U's relegation tag as they headed into the
2013–14 season. During the first half of the season, Dunne gave first-team debuts to
Conor Hubble,
Sammie Szmodics and
Macauley Bonne having already brought
Alex Gilbey,
Freddie Ladapo and
Tosin Olufemi into the first-team picture during the 2012–13 season. Chairman Cowling was pleased that his investments in the youth team had begun producing players that were able to break into the first-team. Dunne was nominated for the
Football League One Manager of the Month award for the month of January 2014 after steering his side into the top-half of the League One table with two high-scoring wins and a solid draw at MK Dons. It was the second time Dunne had been nominated, after being shortlisted in November 2012 but pipped to the prize by
Sheffield United manager
Danny Wilson. Once again however, Dunne was beaten to the accolade, this time by
Leyton Orient boss
Russell Slade. Following a string of four successive defeats and a winless start to the
2014–15 season, Dunne left Colchester United by mutual consent on 1 September 2014, ending his 18-year association with the club. Colchester United chairman Robbie Cowling stated Dunne decided to go as he felt he took things as far as he could.
Cambridge United In 2015, Dunne joined
Cambridge United as assistant to
Shaun Derry. Following Derry's departure in February 2018, Dunne was appointed as interim manager of the club until the end of the season before being officially appointed as manager on a three-year deal in May 2018. However, he was sacked on 1 December 2018 due to poor results leaving the club 21st in the league table.
Bristol Rovers On 22 February 2019, Dunne joined
Graham Coughlan's coaching staff at
Bristol Rovers on a voluntary basis until the end of the season. He was appointed as assistant manager in June 2019. Dunne was caretaker manager of Rovers for the FA Cup second round replay against
Plymouth Argyle where he oversaw a 1-0 win.
Mansfield Town Following Coughlan's departure to
Mansfield Town in December 2019, Dunne joined him at the Nottinghamshire club as assistant manager. Dunne was sacked from the post on 28 October 2020.
Stevenage Dunne joined League Two club
Stevenage on 1 December 2020, taking on the role of assistant manager to
Alex Revell. After a week in his new position, Dunne left his role at the club for personal reasons.
Colchester United In March 2021, Dunne returned to Colchester United to assist interim manager
Wayne Brown. In January 2022, following the return of Wayne Brown as interim manager, Dunne again returned to the club as interim assistant coach. On 17 May 2022, Brown and Dunne were given the job on a permanent basis. On 18 September 2022, Brown and Dunne were sacked by Colchester.
Newport County On 21 October 2022 Dunne was again appointed assistant manager to
Graham Coughlan at League Two Newport County. On 20 June 2024, Coughlan and Dunne departed the club by mutual consent.
Gillingham On 15 November 2024, Dunne returned to League Two club Gillingham, the club where he had started his career, in the role of Youth Team Manager.
Colchester United On 24 February 2026, Dunne was appointed Lead Under 18s Coach at his former club
Colchester United. ==Career statistics==